https://www.cazypedia.org/api.php?action=feedcontributions&feedformat=atom&user=Takatsugu+MiyazakiCAZypedia - User contributions [en-ca]2026-05-05T00:02:34ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=File:Fig1_GH49_substrates.png&diff=19514File:Fig1 GH49 substrates.png2025-09-30T10:43:11Z<p>Takatsugu Miyazaki: Takatsugu Miyazaki uploaded a new version of File:Fig1 GH49 substrates.png</p>
<hr />
<div></div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_49&diff=19513Glycoside Hydrolase Family 492025-09-30T09:19:03Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH49'''<br />
|-<br />
|'''Clan''' <br />
|GH-N<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH49.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[File:Fig1_GH49_substrates.png|thumb|600px|right|'''Figure 1. Substrates of GH49 enzymes.''' All enzymes except dextran 1,6-&alpha;-isomaltotriosidase are endo-acting glycoside hydrolases. Sulfated arabinan contains sulfate groups at 2- and 3-OH (3S) of L-arabinopyranose residue and possesses side chains of galactose and xylose, which are not shown in this figure.]]<br />
<br />
[[Glycoside hydrolases]] of GH49 cleave &alpha;-(1→6)-glucosidic linkages or &alpha;-(1→4)-glucosidic linkages of polysaccharides and oligosaccharides containing &alpha;-(1→6)-glucosidic linkages, such as dextran and pullulan. The major activities reported for this family of glycoside hydrolases are dextranase (EC [{{EClink}}3.2.1.11 3.2.1.11]), and a dextranase from ''Talaromyces minioluteum'' (formerly known as ''Penicillium minioluteum''), Dex49A, is currently the most characterized enzyme. GH49 dextranases have been found in some bacteria and fungi. Dextran 1,6-&alpha;-isomaltotriosidase (EC [{{EClink}}3.2.1.95 3.2.1.95]) from ''Brevibacterium fuscum'' var. ''dextranlyticum'' is an exo-acting enzyme that hydrolyzes dextran from the non-reducing ends to produce isomaltotriose <cite>Mizuno1999</cite>. Isopullulanase (EC [{{EClink}}3.2.1.57 3.2.1.57])from ''Aspergillus brasiliensis'' ATCC 9642 (formerly ''Aspergillus niger'' ATCC 9642) hydrolyzes α-(1→4)-linkages of pullulan to produce isopanose <cite>Sakano1971</cite>. 4-''O''-&alpha;-D-Isomaltooligosaccharylmaltooligosaccharide 1,4-&alpha;-isomaltooligosaccharohydrolase (IMM-4IH, EC 3.2.1.-) from ''Sarocladium kiliense'' possesses more strict substrate specificity than isopullulanase and cannot hydrolyze pullulan <cite>Kitagawa2023</cite>. As an exception, endo-acting sulfated-arabinan hydrolase (EC 3.2.1-) from ''Phocaeicola plebeius'' degrades sulfated arabinan produced by green algae ''Chaetomorpha'' sp. and ''Cladophora'' sp. <cite>Helbert2019</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH49 &alpha;-glycosidases are [[inverting]] enzymes, as first shown by NMR on a dextranase Dex49A from ''Talaromyces minioluteum'' <cite>Larsson2003</cite> . Optical rotation analysis of the hydrolysis of panose by isopullulanase supported the inverting mechanism <cite>Akeboshi2004</cite>.<br />
<br />
== Catalytic Residues ==<br />
Three Asp residues (Asp376, Asp395, and Asp396 in Dex49A) are conserved in the catalytic center of clan GH-N members, GH49 and [[GH28]] enzymes <cite>Larsson2003 Mizuno2008</cite>, which is also the case for [[GH87]] and [[GH110]]. All three of the Asp mutants of ''A. brasiliensis'' isopullulanase, lost their activities <cite>Akeboshi2004</cite>. The [[general acid]] was first identified in Dex49A from ''Talaromyces minioluteum'' as Asp395 following the three-dimensional structure determination. To date, it is unclear whether either (or both) of the Asp residues (Asp376 and Asp396 in Dex49A) acts as a [[general base]] in the reaction of GH49 and [[GH28]] enzymes <cite>Larsson2003 vanSanten1999 Shimizu2002</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Fig2_GH49_structures.png|thumb|800px|center|'''Figure 2. Overall structures of GH49 enzymes.''' (Left to right) ''Aspergillus brasiliensis'' isopullulanase (IPU) in complex with isopanose (PDB ID [{{PDBlink}}2z8g 2Z8G]), ''Talaromyces minioluteum'' dextranase (Dex49A) in complex with isomaltose (PDB ID [{{PDBlink}}1ogm 1OGM]), and ''Arthrobacter oxydans'' dextranase (AoDex) (PDB ID [{{PDBlink}}6nzs 6NZS]).]]<br />
<br />
<br />
[[File:Fig3_GH49_activesites.png|thumb|600px|right|'''Figure 3. Active sites of GH49 enzymes.''' (A-C) Molecular surfaces of Dex49A (A), IPU (B), and AoDex (C) are shown in gray. Amino acid residues and ligands are shown as stick models: catalytic residues, slate blue; residues forming active site clefts: yellow (C-terminal domain) and pink (N-terminal domain); isomaltose and isopanose, green. In (B), the isomaltose molecule (dark green) bound in N448A variant of IPU (PDB ID [{{PDBlink}}3WWG 3WWG] <cite>Miyazaki2015</cite>) is superimposed. (D) The superimposition of the catalytic residues of the three GH49 enzymes. Water molecules interacting with two general base candidates (asterisk) are shown as red sphere.]]<br />
<br />
Three structures of GH49 enzymes are available so far <cite>Larsson2003 Mizuno2008 Ren2019</cite>, and they display a two-domain structure. The N-terminal domain is a &beta;-sandwich and the C-terminal domain adopts a right-handed parallel &beta;-helix. Although GH49, [[GH28]], [[GH87]], and [[GH110]] families contain enzymes with distinct substrate specificities and exhibit low overall sequence homology, they share similar &beta;-helix folds and the three catalytic Asp residues are completely conserved <cite>Larsson2003 Mizuno2008 Itoh2020 McGuire2020</cite>. Each coil forming the cylindrical &beta;-helix fold is composed of three &beta;-sheets, which are named PB1, PB2, and PB3, following the original definition for a PL1 enzyme, pectate lyase C <cite>Yoder1993</cite>.<br />
<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Dextranase from ''Arthrobacter'' sp. CB-8 <cite>Okushima1991</cite>.<br />
;First stereochemistry determination: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First general acid residue identification: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First 3-D structure: Dextranase (Dex49A) from ''Talaromyces minioluteum'' by X-ray crystallography (PDB ID [{{PDBlink}}1ogm 1OGM]) <cite>Larsson2003</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mizuno1999 pmid=10540747<br />
#Larsson2003 pmid=12962629<br />
#Mizuno2008 pmid=18155243<br />
#Akeboshi2004 pmid=15560783<br />
#vanSanten1999 pmid=10521427<br />
#Shimizu2002 pmid=12022868<br />
#Yoder1993 pmid=8502994<br />
#Okushima1991 pmid=1859672<br />
#Sakano1971 Sakano Y, Masuda N, and Kobayashi T. (1971). ''Hydrolysis of Pullulan by a Novel Enzyme from Aspergillus niger'', ''Agric Biol Chem'' 1971;35(6):971-973. https://doi.org/10.1271/bbb1961.35.971<br />
#Helbert2019 pmid=30850540<br />
#Miyazaki2015 pmid=25359784<br />
#Ren2019 pmid=30919632<br />
#Itoh2020 pmid=31788942<br />
#McGuire2020 pmid=33127644<br />
#Kitagawa2023 pmid=36592961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH049]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_49&diff=19512Glycoside Hydrolase Family 492025-09-30T09:14:54Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH49'''<br />
|-<br />
|'''Clan''' <br />
|GH-N<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH49.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[File:Fig1_GH49_substrates.png|thumb|300px|right|'''Figure 1. Substrates of GH49 enzymes.''' All enzymes except dextran 1,6-&alpha;-isomaltotriosidase are endo-acting glycoside hydrolases. Sulfated arabinan contains sulfate groups at 2- and 3-OH (3S) of L-arabinopyranose residue and possesses side chains of galactose and xylose, which are not shown in this figure.]]<br />
<br />
[[Glycoside hydrolases]] of GH49 cleave &alpha;-(1→6)-glucosidic linkages or &alpha;-(1→4)-glucosidic linkages of polysaccharides and oligosaccharides containing &alpha;-(1→6)-glucosidic linkages, such as dextran and pullulan. The major activities reported for this family of glycoside hydrolases are dextranase (EC [{{EClink}}3.2.1.11 3.2.1.11]), and a dextranase from ''Talaromyces minioluteum'' (formerly known as ''Penicillium minioluteum''), Dex49A, is currently the most characterized enzyme. GH49 dextranases have been found in some bacteria and fungi. Dextran 1,6-&alpha;-isomaltotriosidase (EC [{{EClink}}3.2.1.95 3.2.1.95]) from ''Brevibacterium fuscum'' var. ''dextranlyticum'' is an exo-acting enzyme that hydrolyzes dextran from the non-reducing ends to produce isomaltotriose <cite>Mizuno1999</cite>. Isopullulanase (EC [{{EClink}}3.2.1.57 3.2.1.57])from ''Aspergillus brasiliensis'' ATCC 9642 (formerly ''Aspergillus niger'' ATCC 9642) hydrolyzes α-(1→4)-linkages of pullulan to produce isopanose <cite>Sakano1971</cite>. 4-''O''-&alpha;-D-Isomaltooligosaccharylmaltooligosaccharide 1,4-&alpha;-isomaltooligosaccharohydrolase (IMM-4IH, EC 3.2.1.-) from ''Sarocladium kiliense'' possesses more strict substrate specificity than isopullulanase and cannot hydrolyze pullulan <cite>Kitagawa2023</cite>. As an exception, endo-acting sulfated-arabinan hydrolase (EC 3.2.1-) from ''Phocaeicola plebeius'' degrades sulfated arabinan produced by green algae ''Chaetomorpha'' sp. and ''Cladophora'' sp. <cite>Helbert2019</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH49 &alpha;-glycosidases are [[inverting]] enzymes, as first shown by NMR on a dextranase Dex49A from ''Talaromyces minioluteum'' <cite>Larsson2003</cite> . Optical rotation analysis of the hydrolysis of panose by isopullulanase supported the inverting mechanism <cite>Akeboshi2004</cite>.<br />
<br />
== Catalytic Residues ==<br />
Three Asp residues (Asp376, Asp395, and Asp396 in Dex49A) are conserved in the catalytic center of clan GH-N members, GH49 and [[GH28]] enzymes <cite>Larsson2003 Mizuno2008</cite>, which is also the case for [[GH87]] and [[GH110]]. All three of the Asp mutants of ''A. brasiliensis'' isopullulanase, lost their activities <cite>Akeboshi2004</cite>. The [[general acid]] was first identified in Dex49A from ''Talaromyces minioluteum'' as Asp395 following the three-dimensional structure determination. To date, it is unclear whether either (or both) of the Asp residues (Asp376 and Asp396 in Dex49A) acts as a [[general base]] in the reaction of GH49 and [[GH28]] enzymes <cite>Larsson2003 vanSanten1999 Shimizu2002</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Fig2_GH49_structures.png|thumb|600px|center|'''Figure 2. Overall structures of GH49 enzymes.''' (Left to right) ''Aspergillus brasiliensis'' isopullulanase (IPU) in complex with isopanose (PDB ID [{{PDBlink}}2z8g 2Z8G]), ''Talaromyces minioluteum'' dextranase (Dex49A) in complex with isomaltose (PDB ID [{{PDBlink}}1ogm 1OGM]), and ''Arthrobacter oxydans'' dextranase (AoDex) (PDB ID [{{PDBlink}}6nzs 6NZS]).]]<br />
<br />
<br />
[[File:Fig3_GH49_activesites.png|thumb|300px|right|'''Figure 3. Active sites of GH49 enzymes.''' (A-C) Molecular surfaces of Dex49A (A), IPU (B), and AoDex (C) are shown in gray. Amino acid residues and ligands are shown as stick models: catalytic residues, slate blue; residues forming active site clefts: yellow (C-terminal domain) and pink (N-terminal domain); isomaltose and isopanose, green. In (B), the isomaltose molecule (dark green) bound in N448A variant of IPU (PDB ID [{{PDBlink}}3WWG 3WWG] <cite>Miyazaki2015</cite>) is superimposed. (D) The superimposition of the catalytic residues of the three GH49 enzymes. Water molecules interacting with two general base candidates (asterisk) are shown as red sphere.]]<br />
<br />
Three structures of GH49 enzymes are available so far <cite>Larsson2003 Mizuno2008 Ren2019</cite>, and they display a two-domain structure. The N-terminal domain is a &beta;-sandwich and the C-terminal domain adopts a right-handed parallel &beta;-helix. Although GH49, [[GH28]], [[GH87]], and [[GH110]] families contain enzymes with distinct substrate specificities and exhibit low overall sequence homology, they share similar &beta;-helix folds and the three catalytic Asp residues are completely conserved <cite>Larsson2003 Mizuno2008 Itoh2020 McGuire2020</cite>. Each coil forming the cylindrical &beta;-helix fold is composed of three &beta;-sheets, which are named PB1, PB2, and PB3, following the original definition for a PL1 enzyme, pectate lyase C <cite>Yoder1993</cite>.<br />
<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Dextranase from ''Arthrobacter'' sp. CB-8 <cite>Okushima1991</cite>.<br />
;First stereochemistry determination: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First general acid residue identification: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First 3-D structure: Dextranase (Dex49A) from ''Talaromyces minioluteum'' by X-ray crystallography (PDB ID [{{PDBlink}}1ogm 1OGM]) <cite>Larsson2003</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mizuno1999 pmid=10540747<br />
#Larsson2003 pmid=12962629<br />
#Mizuno2008 pmid=18155243<br />
#Akeboshi2004 pmid=15560783<br />
#vanSanten1999 pmid=10521427<br />
#Shimizu2002 pmid=12022868<br />
#Yoder1993 pmid=8502994<br />
#Okushima1991 pmid=1859672<br />
#Sakano1971 Sakano Y, Masuda N, and Kobayashi T. (1971). ''Hydrolysis of Pullulan by a Novel Enzyme from Aspergillus niger'', ''Agric Biol Chem'' 1971;35(6):971-973. https://doi.org/10.1271/bbb1961.35.971<br />
#Helbert2019 pmid=30850540<br />
#Miyazaki2015 pmid=25359784<br />
#Ren2019 pmid=30919632<br />
#Itoh2020 pmid=31788942<br />
#McGuire2020 pmid=33127644<br />
#Kitagawa2023 pmid=36592961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH049]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_49&diff=19511Glycoside Hydrolase Family 492025-09-30T09:09:33Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH49'''<br />
|-<br />
|'''Clan''' <br />
|GH-N<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH49.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[File:Fig1_GH49_substrates.png|thumb|300px|right|'''Figure 1. Substrates of GH49 enzymes.''' All enzymes except dextran 1,6-&alpha;-isomaltotriosidase are endo-acting glycoside hydrolases. Sulfated arabinan contains sulfate groups at 2- and 3-OH (3S) of L-arabinopyranose residue and possesses side chains of galactose and xylose, which are not shown in this figure.]]<br />
<br />
[[Glycoside hydrolases]] of GH49 cleave &alpha;-(1→6)-glucosidic linkages or &alpha;-(1→4)-glucosidic linkages of polysaccharides and oligosaccharides containing &alpha;-(1→6)-glucosidic linkages, such as dextran and pullulan. The major activities reported for this family of glycoside hydrolases are dextranase (EC [{{EClink}}3.2.1.11 3.2.1.11]), and a dextranase from ''Talaromyces minioluteum'' (formerly known as ''Penicillium minioluteum''), Dex49A, is currently the most characterized enzyme. GH49 dextranases have been found in some bacteria and fungi. Dextran 1,6-&alpha;-isomaltotriosidase (EC [{{EClink}}3.2.1.95 3.2.1.95]) from ''Brevibacterium fuscum'' var. ''dextranlyticum'' is an exo-acting enzyme that hydrolyzes dextran from the non-reducing ends to produce isomaltotriose <cite>Mizuno1999</cite>. Isopullulanase (EC [{{EClink}}3.2.1.57 3.2.1.57])from ''Aspergillus brasiliensis'' ATCC 9642 (formerly ''Aspergillus niger'' ATCC 9642) hydrolyzes α-(1→4)-linkages of pullulan to produce isopanose <cite>Sakano1971</cite>. 4-''O''-&alpha;-D-Isomaltooligosaccharylmaltooligosaccharide 1,4-&alpha;-isomaltooligosaccharohydrolase (EC 3.2.1.-) from ''Sarocladium kiliense'' possesses more strict substrate specificity than isopullulanase and cannot hydrolyze pullulan <cite>Kitagawa2023</cite>. As an exception, endo-acting sulfated-arabinan hydrolase (EC 3.2.1-) from ''Phocaeicola plebeius'' degrades sulfated arabinan produced by green algae ''Chaetomorpha'' sp. and ''Cladophora'' sp. <cite>Helbert2019</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH49 &alpha;-glycosidases are [[inverting]] enzymes, as first shown by NMR on a dextranase Dex49A from ''Talaromyces minioluteum'' <cite>Larsson2003</cite> . Optical rotation analysis of the hydrolysis of panose by isopullulanase supported the inverting mechanism <cite>Akeboshi2004</cite>.<br />
<br />
== Catalytic Residues ==<br />
Three Asp residues (Asp376, Asp395, and Asp396 in Dex49A) are conserved in the catalytic center of clan GH-N members, GH49 and [[GH28]] enzymes <cite>Larsson2003 Mizuno2008</cite>, which is also the case for [[GH87]] and [[GH110]]. All three of the Asp mutants of ''A. brasiliensis'' isopullulanase, lost their activities <cite>Akeboshi2004</cite>. The [[general acid]] was first identified in Dex49A from ''Talaromyces minioluteum'' as Asp395 following the three-dimensional structure determination. To date, it is unclear whether either (or both) of the Asp residues (Asp376 and Asp396 in Dex49A) acts as a [[general base]] in the reaction of GH49 and [[GH28]] enzymes <cite>Larsson2003 vanSanten1999 Shimizu2002</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Fig2_GH49_structures.png|thumb|600px|center|'''Figure 2. Overall structures of GH49 enzymes.''' (Left to right) ''Aspergillus brasiliensis'' isopullulanase (IPU) in complex with isopanose (PDB ID [{{PDBlink}}2z8g 2Z8G]), ''Talaromyces minioluteum'' dextranase (Dex49A) in complex with isomaltose (PDB ID [{{PDBlink}}1ogm 1OGM]), and ''Arthrobacter oxydans'' dextranase (AoDex) (PDB ID [{{PDBlink}}6nzs 6NZS]).]]<br />
<br />
<br />
[[File:Fig3_GH49_activesites.png|thumb|300px|right|'''Figure 3. Active sites of GH49 enzymes.''' (A-C) Molecular surfaces of Dex49A (A), IPU (B), and AoDex (C) are shown in gray. Amino acid residues and ligands are shown as stick models: catalytic residues, slate blue; residues forming active site clefts: yellow (C-terminal domain) and pink (N-terminal domain); isomaltose and isopanose, green. In (B), the isomaltose molecule (dark green) bound in N448A variant of IPU (PDB ID [{{PDBlink}}3WWG 3WWG] <cite>Miyazaki2015</cite>) is superimposed. (D) The superimposition of the catalytic residues of the three GH49 enzymes. Water molecules interacting with two general base candidates (asterisk) are shown as red sphere.]]<br />
<br />
Three structures of GH49 enzymes are available so far <cite>Larsson2003 Mizuno2008 Ren2019</cite>, and they display a two-domain structure. The N-terminal domain is a &beta;-sandwich and the C-terminal domain adopts a right-handed parallel &beta;-helix. Although GH49, [[GH28]], [[GH87]], and [[GH110]] families contain enzymes with distinct substrate specificities and exhibit low overall sequence homology, they share similar &beta;-helix folds and the three catalytic Asp residues are completely conserved <cite>Larsson2003 Mizuno2008 Itoh2020 McGuire2020</cite>. Each coil forming the cylindrical &beta;-helix fold is composed of three &beta;-sheets, which are named PB1, PB2, and PB3, following the original definition for a PL1 enzyme, pectate lyase C <cite>Yoder1993</cite>.<br />
<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Dextranase from ''Arthrobacter'' sp. CB-8 <cite>Okushima1991</cite>.<br />
;First stereochemistry determination: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First general acid residue identification: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First 3-D structure: Dextranase (Dex49A) from ''Talaromyces minioluteum'' by X-ray crystallography (PDB ID [{{PDBlink}}1ogm 1OGM]) <cite>Larsson2003</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mizuno1999 pmid=10540747<br />
#Larsson2003 pmid=12962629<br />
#Mizuno2008 pmid=18155243<br />
#Akeboshi2004 pmid=15560783<br />
#vanSanten1999 pmid=10521427<br />
#Shimizu2002 pmid=12022868<br />
#Yoder1993 pmid=8502994<br />
#Okushima1991 pmid=1859672<br />
#Sakano1971 Sakano Y, Masuda N, and Kobayashi T. (1971). ''Hydrolysis of Pullulan by a Novel Enzyme from Aspergillus niger'', ''Agric Biol Chem'' 1971;35(6):971-973. https://doi.org/10.1271/bbb1961.35.971<br />
#Helbert2019 pmid=30850540<br />
#Miyazaki2015 pmid=25359784<br />
#Ren2019 pmid=30919632<br />
#Itoh2020 pmid=31788942<br />
#McGuire2020 pmid=33127644<br />
#Kitagawa2023 pmid=36592961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH049]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_49&diff=19510Glycoside Hydrolase Family 492025-09-30T09:07:38Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH49'''<br />
|-<br />
|'''Clan''' <br />
|GH-N<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH49.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[File:Fig1_GH49_substrates.png|thumb|300px|right|'''Figure 1. Substrates of GH49 enzymes.''' All enzymes except dextran 1,6-&alpha;-isomaltotriosidase are endo-acting glycoside hydrolases. Sulfated arabinan contains sulfate groups at 2- and 3-OH (3S) of L-arabinopyranose residue and possesses side chains of galactose and xylose, which are not shown in this figure.]]<br />
<br />
[[Glycoside hydrolases]] of GH49 cleave &alpha;-(1→6)-glucosidic linkages or &alpha;-(1→4)-glucosidic linkages of polysaccharides and oligosaccharides containing &alpha;-(1→6)-glucosidic linkages, such as dextran and pullulan. The major activities reported for this family of glycoside hydrolases are dextranase (EC [{{EClink}}3.2.1.11 3.2.1.11]), and a dextranase from ''Talaromyces minioluteum'' (formerly known as ''Penicillium minioluteum''), Dex49A, is currently the most characterized enzyme. GH49 dextranases have been found in some bacteria and fungi. Dextran 1,6-&alpha;-isomaltotriosidase (EC [{{EClink}}3.2.1.95 3.2.1.95]) from ''Brevibacterium fuscum'' var. ''dextranlyticum'' is an exo-acting enzyme that hydrolyzes dextran from the non-reducing ends to produce isomaltotriose <cite>Mizuno1999</cite>. Isopullulanase (EC [{{EClink}}3.2.1.57 3.2.1.57])from ''Aspergillus brasiliensis'' ATCC 9642 (formerly ''Aspergillus niger'' ATCC 9642) hydrolyzes α-(1→4)-linkages of pullulan to produce isopanose <cite>Sakano1971</cite>. 4-''O''-&alpha;-D-Isomaltooligosaccharylmaltooligosaccharide 1,4-&alpha;-isomaltooligosaccharohydrolase (EC 3.2.1.-) from ''Sarocladium kiliense'' possesses more strict substrate specificity than isopullulanase and cannot hydrolyze pullulan <cite>Kitagawa2023</cite>. As an exception, endo-acting sulfated-arabinan hydrolase (EC 3.2.1-) from ''Phocaeicola plebeius'' degrades sulfated arabinan produced by green algae ''Chaetomorpha'' sp. and ''Cladophora'' sp. <cite>Helbert2019</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH49 &alpha;-glycosidases are [[inverting]] enzymes, as first shown by NMR on a dextranase Dex49A from ''Talaromyces minioluteum'' <cite>Larsson2003</cite> . Optical rotation analysis of the hydrolysis of panose by isopullulanase supported the inverting mechanism <cite>Akeboshi2004</cite>.<br />
<br />
== Catalytic Residues ==<br />
Three Asp residues (Asp376, Asp395, and Asp396 in Dex49A) are conserved in the catalytic center of clan GH-N members, GH49 and [[GH28]] enzymes <cite>Larsson2003 Mizuno2008</cite>, which is also the case for [[GH87]] and [[GH110]]. All three of the Asp mutants of ''A. brasiliensis'' isopullulanase, lost their activities <cite>Akeboshi2004</cite>. The [[general acid]] was first identified in Dex49A from ''Talaromyces minioluteum'' as Asp395 following the three-dimensional structure determination. To date, it is unclear whether either (or both) of the Asp residues (Asp376 and Asp396 in Dex49A) acts as a [[general base]] in the reaction of GH49 and [[GH28]] enzymes <cite>Larsson2003 vanSanten1999 Shimizu2002</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Fig2_GH49_structures.png|thumb|600px|center|'''Figure 2. Overall structures of GH49 enzymes.''' (Left to right) ''Aspergillus brasiliensis'' isopullulanase (IPU) in complex with isopanose (PDB ID [{{PDBlink}}2z8g 2Z8G]), ''Talaromyces minioluteum'' dextranase (Dex49A) in complex with isomaltose (PDB ID [{{PDBlink}}1ogm 1OGM]), and ''Arthrobacter oxydans'' dextranase (AoDex) (PDB ID [{{PDBlink}}6nzs 6NZS]).]]<br />
<br />
<br />
[[File:Fig3_GH49_activesites.png|thumb|300px|right|'''Figure 3. Active sites of GH49 enzymes.''' (A-C) Molecular surfaces of Dex49A (A), IPU (B), and AoDex (C) are shown in gray. Amino acid residues and ligands are shown as stick models: catalytic residues, slate blue; residues forming active site clefts: yellow (C-terminal domain) and pink (N-terminal domain); isomaltose and isopanose, green. In (B), the isomaltose molecule (dark green) bound in N448A variant of IPU (PDB ID [{{PDBlink}}3WWG 3WWG]) is superimposed. (D) The superimposition of the catalytic residues of the three GH49 enzymes. Water molecules interacting with two general base candidates (asterisk) are shown as red sphere.]]<br />
<br />
Three structures of GH49 enzymes are available so far <cite>Larsson2003 Mizuno2008 Ren2019</cite>, and they display a two-domain structure. The N-terminal domain is a &beta;-sandwich and the C-terminal domain adopts a right-handed parallel &beta;-helix. Although GH49, [[GH28]], [[GH87]], and [[GH110]] families contain enzymes with distinct substrate specificities and exhibit low overall sequence homology, they share similar &beta;-helix folds and the three catalytic Asp residues are completely conserved <cite>Larsson2003 Mizuno2008 Itoh2020 McGuire2020</cite>. Each coil forming the cylindrical &beta;-helix fold is composed of three &beta;-sheets, which are named PB1, PB2, and PB3, following the original definition for a PL1 enzyme, pectate lyase C <cite>Yoder1993</cite>.<br />
<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Dextranase from ''Arthrobacter'' sp. CB-8 <cite>Okushima1991</cite>.<br />
;First stereochemistry determination: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First general acid residue identification: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First 3-D structure: Dextranase (Dex49A) from ''Talaromyces minioluteum'' by X-ray crystallography (PDB ID [{{PDBlink}}1ogm 1OGM]) <cite>Larsson2003</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mizuno1999 pmid=10540747<br />
#Larsson2003 pmid=12962629<br />
#Mizuno2008 pmid=18155243<br />
#Akeboshi2004 pmid=15560783<br />
#vanSanten1999 pmid=10521427<br />
#Shimizu2002 pmid=12022868<br />
#Yoder1993 pmid=8502994<br />
#Okushima1991 pmid=1859672<br />
#Sakano1971 Sakano Y, Masuda N, and Kobayashi T. (1971). ''Hydrolysis of Pullulan by a Novel Enzyme from Aspergillus niger'', ''Agric Biol Chem'' 1971;35(6):971-973. https://doi.org/10.1271/bbb1961.35.971<br />
#Helbert2019 pmid=30850540<br />
#Ren2019 pmid=30919632<br />
#Itoh2020 pmid=31788942<br />
#McGuire2020 pmid=33127644<br />
#Kitagawa2023 pmid=36592961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH049]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_49&diff=19509Glycoside Hydrolase Family 492025-09-30T08:50:57Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH49'''<br />
|-<br />
|'''Clan''' <br />
|GH-N<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH49.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of GH49 cleave &alpha;-(1→6)-glucosidic linkages or &alpha;-(1→4)-glucosidic linkages of polysaccharides and oligosaccharides containing &alpha;-(1→6)-glucosidic linkages, such as dextran and pullulan. The major activities reported for this family of glycoside hydrolases are dextranase (EC [{{EClink}}3.2.1.11 3.2.1.11]), and a dextranase from ''Talaromyces minioluteum'' (formerly known as ''Penicillium minioluteum''), Dex49A, is currently the most characterized enzyme. GH49 dextranases have been found in some bacteria and fungi. Dextran 1,6-&alpha;-isomaltotriosidase (EC [{{EClink}}3.2.1.95 3.2.1.95]) from ''Brevibacterium fuscum'' var. ''dextranlyticum'' is an exo-acting enzyme that hydrolyzes dextran from the non-reducing ends to produce isomaltotriose <cite>Mizuno1999</cite>. Isopullulanase (EC [{{EClink}}3.2.1.57 3.2.1.57])from ''Aspergillus brasiliensis'' ATCC 9642 (formerly ''Aspergillus niger'' ATCC 9642) hydrolyzes α-(1→4)-linkages of pullulan to produce isopanose <cite>Sakano1971</cite>. 4-O-&alpha;-D-Isomaltooligosaccharylmaltooligosaccharide 1,4-&alpha;-isomaltooligosaccharohydrolase (EC 3.2.1.-) from ''Sarocladium kiliense'' possesses more strict substrate specificity than isopullulanase and cannot hydrolyze pullulan <cite>Kitagawa2023</cite>. As an exception, endo-acting sulfated-arabinan hydrolase (EC 3.2.1-) from ''Phocaeicola plebeius'' degrades sulfated arabinan produced by green algae ''Chaetomorpha'' sp. and ''Cladophora'' sp. <cite>Helbert2019</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH49 &alpha;-glycosidases are [[inverting]] enzymes, as first shown by NMR on a dextranase Dex49A from ''Talaromyces minioluteum'' <cite>Larsson2003</cite> . Optical rotation analysis of the hydrolysis of panose by isopullulanase supported the inverting mechanism <cite>Akeboshi2004</cite>.<br />
<br />
== Catalytic Residues ==<br />
Three Asp residues (Asp376, Asp395, and Asp396 in Dex49A) are conserved in the catalytic center of clan GH-N members, GH49 and [[GH28]] enzymes <cite>Larsson2003 Mizuno2008</cite>, which is also the case for [[GH87]] and [[GH110]]. All three of the Asp mutants of ''A. brasiliensis'' isopullulanase, lost their activities <cite>Akeboshi2004</cite>. The [[general acid]] was first identified in Dex49A from ''Talaromyces minioluteum'' as Asp395 following the three-dimensional structure determination. To date, it is unclear whether either (or both) of the Asp residues (Asp376 and Asp396 in Dex49A) acts as a [[general base]] in the reaction of GH49 and [[GH28]] enzymes <cite>Larsson2003 vanSanten1999 Shimizu2002</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Three structures of GH49 enzymes are available so far <cite>Larsson2003 Mizuno2008 Ren2019</cite>, and they display a two-domain structure. The N-terminal domain is a &beta;-sandwich and the C-terminal domain adopts a right-handed parallel &beta;-helix. Although GH49, [[GH28]], [[GH87]], and [[GH110]] families contain enzymes with distinct substrate specificities and exhibit low overall sequence homology, they share similar &beta;-helix folds and the three catalytic Asp residues are completely conserved <cite>Larsson2003 Mizuno2008 Itoh2020 McGuire2020</cite>. Each coil forming the cylindrical &beta;-helix fold is composed of three &beta;-sheets, which are named PB1, PB2, and PB3, following the original definition for a PL1 enzyme, pectate lyase C <cite>Yoder1993</cite>.<br />
<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Dextranase from ''Arthrobacter'' sp. CB-8 <cite>Okushima1991</cite>.<br />
;First stereochemistry determination: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First general acid residue identification: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First 3-D structure: Dextranase (Dex49A) from ''Talaromyces minioluteum'' by X-ray crystallography (PDB ID [{{PDBlink}}1ogm 1OGM]) <cite>Larsson2003</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mizuno1999 pmid=10540747<br />
#Larsson2003 pmid=12962629<br />
#Mizuno2008 pmid=18155243<br />
#Akeboshi2004 pmid=15560783<br />
#vanSanten1999 pmid=10521427<br />
#Shimizu2002 pmid=12022868<br />
#Yoder1993 pmid=8502994<br />
#Okushima1991 pmid=1859672<br />
#Sakano1971 Sakano Y, Masuda N, and Kobayashi T. (1971). ''Hydrolysis of Pullulan by a Novel Enzyme from Aspergillus niger'', ''Agric Biol Chem'' 1971;35(6):971-973. https://doi.org/10.1271/bbb1961.35.971<br />
#Helbert2019 pmid=30850540<br />
#Ren2019 pmid=30919632<br />
#Itoh2020 pmid=31788942<br />
#McGuire2020 pmid=33127644<br />
#Kitagawa2023 pmid=36592961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH049]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=File:Fig3_GH49_activesites.png&diff=19508File:Fig3 GH49 activesites.png2025-09-30T08:24:03Z<p>Takatsugu Miyazaki: </p>
<hr />
<div></div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=File:Fig2_GH49_structures.png&diff=19507File:Fig2 GH49 structures.png2025-09-30T08:23:45Z<p>Takatsugu Miyazaki: </p>
<hr />
<div></div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=File:Fig1_GH49_substrates.png&diff=19506File:Fig1 GH49 substrates.png2025-09-30T08:23:03Z<p>Takatsugu Miyazaki: </p>
<hr />
<div></div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=19499User:Takatsugu Miyazaki2025-09-05T05:14:55Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Associate Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase (CcCel6C) <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase (CcCel6A) <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase (BmSUH) <cite>Miyazaki2020a</cite><br />
*[[GH16]]_16 ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase (AgIMD) <cite>Okazawa2015</cite><br />
*[[GH31]]_14 ''Pseudopedobacter saltans'' α-galactosidase (PsGal31A) '''Subfamily First''' <cite>Miyazaki2015a</cite><br />
*[[GH31]]_15 ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase (LlGH31_u1) '''Subfamily First''' <cite>Ikegaya2022</cite><br />
*[[GH31]]_18 ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase (EfNag31A) '''Subfamily First''' <cite>Miyazaki2020b Miyazaki2022a</cite><br />
*[[GH31]]_19 ''Bacteroides salyersiae'' and ''Flavihumibacter petaseus'' α-1,4-galactosidases (BsGH31_19 and FpGH31_19) '''Subfamily First''' <cite>Ikegaya2023</cite><br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase (CcAbf62A) <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase (Tt8MGH) <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase (FjGH65A) <cite>Nakamura2021 Nakamura2023</cite><br />
*[[GH66]] ''Flavobacterium johnsoniae'' dextranase (FjGH66) <cite>Nakamura2023</cite><br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (EfGH92, Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH97]] ''Flavobacterium johnsoniae'' glucodextranase (FjGH97A) <cite>Nakamura2024</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH27]] ''Flavobacterium johnsoniae'' dextranase (FjGH27A) <cite>Nakamura2025</cite><br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase (BmFucA) <cite>Nakamura2020</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase (FjDex31A) <cite>Gozu2016 Nakamura2023</cite><br />
*[[GH31]]_10 ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase (Ps6GT31A) <cite>Ichinose2017</cite><br />
*[[GH31]]_14 ''Pedobacter heparinus'' α-galactosidase (PhGal31A) <cite>Miyazaki2015a</cite><br />
*[[GH31]]_15 ''Cordyceps militaris'' α-1,3-glucosidase (CmGH31_u1) <cite>Ikegaya2022</cite><br />
*[[GH31]]_18 ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase (BmNag31) <cite>Ikegaya2021</cite><br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme (MdDDE) <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase (PsDEX598) <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
<br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
#Nakamura2023 pmid=37269952<br />
#Ikegaya2023 pmid=37438884<br />
#Nakamura2024 pmid=38661728<br />
#Nakamura2025 pmid=40905719<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17965User:Takatsugu Miyazaki2024-04-28T07:37:07Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Associate Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]]_16 ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]]_14 ''Pseudopedobacter saltans'' α-galactosidase '''Subfamily First''' <cite>Miyazaki2015a</cite><br />
*[[GH31]]_15 ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase '''Subfamily First''' <cite>Ikegaya2022</cite><br />
*[[GH31]]_18 ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase '''Subfamily First''' <cite>Miyazaki2020b Miyazaki2022a</cite><br />
*[[GH31]]_19 ''Bacteroides salyersiae'' and ''Flavihumibacter petaseus'' α-1,4-galactosidases '''Subfamily First''' <cite>Ikegaya2023</cite><br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021 Nakamura2023</cite><br />
*[[GH66]] ''Flavobacterium johnsoniae'' dextranase <cite>Nakamura2023</cite><br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH97]] ''Flavobacterium johnsoniae'' glucodextranase <cite>Nakamura2024</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016 Nakamura2023</cite><br />
*[[GH31]]_10 ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
*[[GH31]]_14 ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
*[[GH31]]_15 ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
*[[GH31]]_18 ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
<br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
#Nakamura2023 pmid=37269952<br />
#Ikegaya2023 pmid=37438884<br />
#Nakamura2024 pmid=38661728<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17942User:Takatsugu Miyazaki2024-04-18T09:16:03Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Associate Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]]_16 ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]]_14 ''Pseudopedobacter saltans'' α-galactosidase '''Subfamily First''' <cite>Miyazaki2015a</cite><br />
*[[GH31]]_15 ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase '''Subfamily First''' <cite>Ikegaya2022</cite><br />
*[[GH31]]_18 ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase '''Subfamily First''' <cite>Miyazaki2020b Miyazaki2022a</cite><br />
*[[GH31]]_19 ''Bacteroides salyersiae'' and ''Flavihumibacter petaseus'' α-1,4-galactosidases '''Subfamily First''' <cite>Ikegaya2023</cite><br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021 Nakamura2023</cite><br />
*[[GH66]] ''Flavobacterium johnsoniae'' dextranase <cite>Nakamura2023</cite><br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
<br />
*[[GH97]] ''Flavobacterium johnsoniae'' glucodextranase<br />
<br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016 Nakamura2023</cite><br />
*[[GH31]]_10 ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
*[[GH31]]_14 ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
*[[GH31]]_15 ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
*[[GH31]]_18 ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
<br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
#Nakamura2023 pmid=37269952<br />
#Ikegaya2023 pmid=37438884<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17450User:Takatsugu Miyazaki2023-07-15T05:47:36Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Associate Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]]_16 ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]]_14 ''Pseudopedobacter saltans'' α-galactosidase '''Subfamily First''' <cite>Miyazaki2015a</cite><br />
*[[GH31]]_15 ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase '''Subfamily First''' <cite>Ikegaya2022</cite><br />
*[[GH31]]_18 ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase '''Subfamily First''' <cite>Miyazaki2020b Miyazaki2022a</cite><br />
*[[GH31]]_19 ''Bacteroides salyersiae'' and ''Flavihumibacter petaseus'' α-1,4-galactosidases '''Subfamily First''' <cite>Ikegaya2023</cite><br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021 Nakamura2023</cite><br />
*[[GH66]] ''Flavobacterium johnsoniae'' dextranase <cite>Nakamura2023</cite><br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016 Nakamura2023</cite><br />
*[[GH31]]_10 ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
*[[GH31]]_14 ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
*[[GH31]]_15 ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
*[[GH31]]_18 ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
<br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
#Nakamura2023 pmid=37269952<br />
#Ikegaya2023 pmid=37438884<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17449User:Takatsugu Miyazaki2023-07-15T05:45:21Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Associate Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]]_16 ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]]_14 ''Pseudopedobacter saltans'' α-galactosidase '''Subfamily First''' <cite>Miyazaki2015a</cite><br />
<br />
*[[GH31]]_15 ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase '''Subfamily First''' <cite>Ikegaya2022</cite><br />
<br />
*[[GH31]]_18 ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase '''Subfamily First''' <cite>Miyazaki2020b Miyazaki2022a</cite><br />
*[[GH31]]_19 ''Bacteroides salyersiae'' and ''Flavihumibacter petaseus'' α-1,4-galactosidases '''Subfamily First''' <cite>Ikegaya2023</cite><br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021 Nakamura2023</cite><br />
<br />
*[[GH66]] ''Flavobacterium johnsoniae'' dextranase <cite>Nakamura2023</cite><br />
<br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
<br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016 Nakamura2023</cite><br />
*[[GH31]]_10 ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
<br />
*[[GH31]]_14 ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
<br />
*[[GH31]]_15 ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
<br />
*[[GH31]]_18 ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
<br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
#Nakamura2023 pmid=37269952<br />
#Ikegaya2023 pmid=37438884<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_63&diff=17440Glycoside Hydrolase Family 632023-07-12T06:00:45Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH63'''<br />
|-<br />
|'''Clan''' <br />
|GH-G<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|Inferred<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH63.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of GH63 are exo-acting &alpha;-glucosidases. Eukaryotic members of this family are processing &alpha;-glucosidase I enzymes (mannosyl-oligosaccharide glucosidase, EC [{{EClink}}3.2.1.106 3.2.1.106]), which specifically hydrolyze the terminal &alpha;-1,2-glucosidic linkage in the ''N''-linked oligosaccharide precursor, Glc<sub>3</sub>Man<sub>9</sub>GlcNAc<sub>2</sub>, to produce &beta;-glucose and Glc<sub>2</sub>Man<sub>9</sub>GlcNAc<sub>2</sub>. Processing &alpha;-glucosidase I thus plays a critical role in the maturation of eukaryotic ''N''-glycans. The enzymatic properties of Cwh41p, a processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'', have been intensively studied <cite>Dhanawansa2002</cite> (also reviewed in <cite>Herscovics1999</cite>).<br />
<br />
Genes encoding GH63 enzymes have also been found in archaea and bacteria, but their natural substrates are still unclear, as these organisms are not known to produce eukaryotic ''N''-linked oligosacharides. A bacterial GH63 enzyme, ''Escherichia coli'' YgjK, demonstrated the highest activity toward the &alpha;-1,3-glucosidic linkage of nigerose (Glc-&alpha;-1,3-Glc) among the commercially available sugars tested, but the ''K''<sub>m</sub> value for nigerose was substantially higher than that for other typical &alpha;-glucosidases <cite>Kurakata2008</cite>. The aglycon specificity of YgjK was screened using its glycosynthase mutants (D324N and E727A), which synthesized 2-''O''-α-glucopyranosylgalactose from β-glucopyranosyl fluoride donor and galactose acceptor <cite>Miyazaki2013</cite>.<br />
<br />
In 2013, the substrates of GH63 enzymes from ''Thermus thermophilus'' HB27 and ''Rubrobacter radiotolerans'' RSPS-4 were identified as compatible solutes, &alpha;-D-mannopyranosyl-1,2-D-glycerate (mannosylglycerate) and &alpha;-D-glucopyranosyl-1,2-D-glycerate (glucosylglycerate) <cite>Alarico2013</cite>. Subsequently, glucosylglycerate hydrolase was identified in ''Mycobacterium hassiacum'' and was found to be involved in the recovery process from nitrogen starvation by hydrolyzing glucosylglycerate <cite>Alarico2014</cite>.<br />
<br />
An orthologous gene for mannosyl/glucosylglycerate hydrolase was also found in the genome of plant ''Selaginella moellendorffii'', and the gene product hydrolyzed these compatible solutes <cite>Nobre2013</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH63 enzymes are [[inverting]] enzymes, as first shown by NMR on a processing &alpha;-glucosidase I from ''S. cerevisiae'' <cite>Palcic1999</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were inferred by comparing the catalytic (&alpha;/&alpha;)<sub>6</sub> barrel domain of the GH63 enzyme, ''E. coli'' YgjK, with those of [[GH15]] and [[GH37]] enzymes. In the case of [[GH37]] and GH63, both of which belong to [[clan]] GH-G, the catalytic [[general acid]] is predicted as an Asp residue (Asp501 in ''E. coli'' YgjK), and the [[general base]] is considered to be a Glu residue (Glu727 in ''E. coli'' YgjK) <cite>Kurakata2008</cite>. Although both of the corresponding residues of [[GH15]], which belongs to [[clan]] GH-L, are identified as Glu residues, the positions of the catalytic residues of [[GH15]], [[GH37]], and GH63 are highly conserved <cite>Kurakata2008 Gibson2007</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of the bacterial GH63 proteins, ''E. coli'' YgjK <cite>Kurakata2008</cite> ([http://www.cazy.org/GH63_structure.html multiple PDB entries]) and ''Thermus thermophilus'' uncharacterised protein TTHA0978 ([{{PDBlink}}2z07 PDB 2z07]), have been reported. The catalytic domain consists of an (&alpha;/&alpha;)<sub>6</sub> barrel fold. The main chain of the (&alpha;/&alpha;)<sub>6</sub> barrel domain shares high structural similarity with those of [[GH15]], [[GH37]], [[GH65]], and [[GH94]] <cite>Kurakata2008 Gibson2007</cite>. This similarity had been predicted on the basis of sequence comparison, before their crystal structures were available <cite>Stam2005</cite>. The first crystal structure of the eukaryotic processing &alpha;-glucosidase I ([{{PDBlink}}4j5t PDB 4j5t]) has been reported in 2013 <cite>Barker2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Human processing &alpha;-glucosidase I <cite>Kalz-Fuller1995</cite>.<br />
;First stereochemistry determination: Processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'' (Cwh41p) <cite>Palcic1999</cite>.<br />
;First general acid residue identification: Inferred from structural comparison <cite>Kurakata2008</cite>.<br />
;First general base residue identification: Inferred from structural comparison <cite>Kurakata2008</cite>.<br />
;First 3-D structure: ''Escherichia coli'' YgjK, an enzyme showing the highest activity for the &alpha;-1,3-glucosidic linkage of nigerose <cite>Kurakata2008</cite>.<br />
;First 3-D structure of a eukaryotic GH63 enzyme: A transmembrane-deleted form of processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'' <cite>Barker2013</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Alarico2013 pmid=23273275<br />
#Barker2013 pmid=23536181<br />
#Dhanawansa2002 pmid=11971867<br />
#Herscovics1999 pmid=9878780<br />
#Kurakata2008 pmid=18586271<br />
#Palcic1999 pmid=10619707<br />
#Gibson2007 pmid=17455176<br />
#Stam2005 pmid=16226731<br />
#Kalz-Fuller1995 pmid=7635146<br />
<br />
#Miyazaki2013 pmid=23826932<br />
<br />
#Nobre2013 pmid=23179444<br />
<br />
#Alarico2014 pmid=25341489<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH063]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_63&diff=17439Glycoside Hydrolase Family 632023-07-12T05:59:50Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH63'''<br />
|-<br />
|'''Clan''' <br />
|GH-G<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|Inferred<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH63.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of GH63 are exo-acting &alpha;-glucosidases. Eukaryotic members of this family are processing &alpha;-glucosidase I enzymes (mannosyl-oligosaccharide glucosidase, EC [{{EClink}}3.2.1.106 3.2.1.106]), which specifically hydrolyze the terminal &alpha;-1,2-glucosidic linkage in the ''N''-linked oligosaccharide precursor, Glc<sub>3</sub>Man<sub>9</sub>GlcNAc<sub>2</sub>, to produce &beta;-glucose and Glc<sub>2</sub>Man<sub>9</sub>GlcNAc<sub>2</sub>. Processing &alpha;-glucosidase I thus plays a critical role in the maturation of eukaryotic ''N''-glycans. The enzymatic properties of Cwh41p, a processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'', have been intensively studied <cite>Dhanawansa2002</cite> (also reviewed in <cite>Herscovics1999</cite>).<br />
<br />
Genes encoding GH63 enzymes have also been found in archaea and bacteria, but their natural substrates are still unclear, as these organisms are not known to produce eukaryotic ''N''-linked oligosacharides. A bacterial GH63 enzyme, ''Escherichia coli'' YgjK, demonstrated the highest activity toward the &alpha;-1,3-glucosidic linkage of nigerose (Glc-&alpha;-1,3-Glc) among the commercially available sugars tested, but the ''K''<sub>m</sub> value for nigerose was substantially higher than that for other typical &alpha;-glucosidases <cite>Kurakata2008</cite>. The aglycon specificity of YgjK was screened using its glycosynthase mutants (D324N and E727A), which synthesized 2-''O''-α-glucopyranosylgalactose from β-glucopyranosyl fluoride donor and galactose acceptor <cite>Miyazaki2013</cite>.<br />
<br />
In 2013, the substrates of GH63 enzymes from ''Thermus thermophilus'' HB27 and ''Rubrobacter radiotolerans'' RSPS-4 were identified as compatible solutes, &alpha;-D-mannopyranosyl-1,2-D-glycerate (mannosylglycerate) and &alpha;-D-glucopyranosyl-1,2-D-glycerate (glucosylglycerate) <cite>Alarico2013</cite>. Subsequently, glucosylglycerate hydrolase was identified in ''Mycobacterium hassiacum'' and was found to be involved in the recovery process from nitrogen starvation by hydrolyzing glucosylglycerate <cite>Alarico2014</cite>.<br />
<br />
An orthologous gene for mannosyl/glucosylglycerate hydrolase was also found in the genome of plant ''Selaginella moellendorffii'', and the gene product hydrolyzed these compatible solutes <cite>Nobre2013</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH63 enzymes are [[inverting]] enzymes, as first shown by NMR on a processing &alpha;-glucosidase I from ''S. cerevisiae'' <cite>Palcic1999</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were inferred by comparing the catalytic (&alpha;/&alpha;)<sub>6</sub> barrel domain of the GH63 enzyme, ''E. coli'' YgjK, with those of [[GH15]] and [[GH37]] enzymes. In the case of [[GH37]] and GH63, both of which belong to [[clan]] GH-G, the catalytic [[general acid]] is predicted as an Asp residue (Asp501 in ''E. coli'' YgjK), and the [[general base]] is considered to be a Glu residue (Glu727 in ''E. coli'' YgjK) <cite>Kurakata2008</cite>. Although both of the corresponding residues of [[GH15]], which belongs to [[clan]] GH-L, are identified as Glu residues, the positions of the catalytic residues of [[GH15]], [[GH37]], and GH63 are highly conserved <cite>Kurakata2008 Gibson2007</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of the bacterial GH63 proteins, ''E. coli'' YgjK <cite>Kurakata2008</cite> ([http://www.cazy.org/GH63_structure.html multiple PDB entries]) and ''Thermus thermophilus'' uncharacterised protein TTHA0978 ([{{PDBlink}}2z07 PDB 2z07]), have been reported. The catalytic domain consists of an (&alpha;/&alpha;)<sub>6</sub> barrel fold. The main chain of the (&alpha;/&alpha;)<sub>6</sub> barrel domain shares high structural similarity with those of [[GH15]], [[GH37]], [[GH65]], and [[GH94]] <cite>Kurakata2008 Gibson2007</cite>. This similarity had been predicted on the basis of sequence comparison, before their crystal structures were available <cite>Stam2005</cite>. The first crystal structure of the eukaryotic processing &alpha;-glucosidase I ([{{PDBlink}}4j5t PDB 4j5t]) has been reported in 2013 <cite>Barker2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Human processing &alpha;-glucosidase I <cite>Kalz-Fuller1995</cite>.<br />
;First stereochemistry determination: Processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'' (Cwh41p) <cite>Palcic1999</cite>.<br />
;First general acid residue identification: Inferred from structural comparison <cite>Kurakata2008</cite>.<br />
;First general base residue identification: Inferred from structural comparison <cite>Kurakata2008</cite>.<br />
;First 3-D structure: ''Escherichia coli'' YgjK, an enzyme showing the highest activity for the &alpha;-1,3-glucosidic linkage of nigerose <cite>Kurakata2008</cite>.<br />
;First 3-D structure of a eukaryotic GH63 enzyme: A transmembrane-deleted form of processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'' <cite>Barker2013</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Alarico2013 pmid=23273275<br />
#Barker2013 pmid=23536181<br />
#Dhanawansa2002 pmid=11971867<br />
#Herscovics1999 pmid=9878780<br />
#Kurakata2008 pmid=18586271<br />
#Palcic1999 pmid=10619707<br />
#Gibson2007 pmid=17455176<br />
#Stam2005 pmid=16226731<br />
#Kalz-Fuller1995 pmid=7635146<br />
<br />
#Miyazaki2013 pmid=23826932<br />
<br />
#Nobre2013 pmid=23179444<br />
<br />
#Alarico2014 pmid=<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH063]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_63&diff=17438Glycoside Hydrolase Family 632023-07-12T05:57:40Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH63'''<br />
|-<br />
|'''Clan''' <br />
|GH-G<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|Inferred<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH63.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of GH63 are exo-acting &alpha;-glucosidases. Eukaryotic members of this family are processing &alpha;-glucosidase I enzymes (mannosyl-oligosaccharide glucosidase, EC [{{EClink}}3.2.1.106 3.2.1.106]), which specifically hydrolyze the terminal &alpha;-1,2-glucosidic linkage in the ''N''-linked oligosaccharide precursor, Glc<sub>3</sub>Man<sub>9</sub>GlcNAc<sub>2</sub>, to produce &beta;-glucose and Glc<sub>2</sub>Man<sub>9</sub>GlcNAc<sub>2</sub>. Processing &alpha;-glucosidase I thus plays a critical role in the maturation of eukaryotic ''N''-glycans. The enzymatic properties of Cwh41p, a processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'', have been intensively studied <cite>Dhanawansa2002</cite> (also reviewed in <cite>Herscovics1999</cite>).<br />
<br />
Genes encoding GH63 enzymes have also been found in archaea and bacteria, but their natural substrates are still unclear, as these organisms are not known to produce eukaryotic ''N''-linked oligosacharides. A bacterial GH63 enzyme, ''Escherichia coli'' YgjK, demonstrated the highest activity toward the &alpha;-1,3-glucosidic linkage of nigerose (Glc-&alpha;-1,3-Glc) among the commercially available sugars tested, but the ''K''<sub>m</sub> value for nigerose was substantially higher than that for other typical &alpha;-glucosidases <cite>Kurakata2008</cite>. The aglycon specificity of YgjK was screened using its glycosynthase mutants (D324N and E727A), which synthesized 2-''O''-α-glucopyranosylgalactose from β-glucopyranosyl fluoride donor and galactose acceptor <cite>Miyazaki2013</cite>.<br />
<br />
In 2013, the substrates of GH63 enzymes from ''Thermus thermophilus'' HB27 and ''Rubrobacter radiotolerans'' RSPS-4 were identified as compatible solutes, &alpha;-D-mannopyranosyl-1,2-D-glycerate (mannosylglycerate) and &alpha;-D-glucopyranosyl-1,2-D-glycerate (glucosylglycerate) <cite>Alarico2013</cite>. Subsequently, glucosylglycerate hydrolase was identified in ''Mycobacterium hassiacum'' and was found to be involved in the recovery process from nitrogen starvation by hydrolyzing glucosylglycerate <cite>Alarico2014</cite>.<br />
<br />
An orthologous gene for mannosyl/glucosylglycerate hydrolase was found in the genome of plant ''Selaginella moellendorffii'', and the gene product hydrolyzed these compatible solutes <cite>Nobre2013</cite>.<br />
== Kinetics and Mechanism ==<br />
Family GH63 enzymes are [[inverting]] enzymes, as first shown by NMR on a processing &alpha;-glucosidase I from ''S. cerevisiae'' <cite>Palcic1999</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were inferred by comparing the catalytic (&alpha;/&alpha;)<sub>6</sub> barrel domain of the GH63 enzyme, ''E. coli'' YgjK, with those of [[GH15]] and [[GH37]] enzymes. In the case of [[GH37]] and GH63, both of which belong to [[clan]] GH-G, the catalytic [[general acid]] is predicted as an Asp residue (Asp501 in ''E. coli'' YgjK), and the [[general base]] is considered to be a Glu residue (Glu727 in ''E. coli'' YgjK) <cite>Kurakata2008</cite>. Although both of the corresponding residues of [[GH15]], which belongs to [[clan]] GH-L, are identified as Glu residues, the positions of the catalytic residues of [[GH15]], [[GH37]], and GH63 are highly conserved <cite>Kurakata2008 Gibson2007</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of the bacterial GH63 proteins, ''E. coli'' YgjK <cite>Kurakata2008</cite> ([http://www.cazy.org/GH63_structure.html multiple PDB entries]) and ''Thermus thermophilus'' uncharacterised protein TTHA0978 ([{{PDBlink}}2z07 PDB 2z07]), have been reported. The catalytic domain consists of an (&alpha;/&alpha;)<sub>6</sub> barrel fold. The main chain of the (&alpha;/&alpha;)<sub>6</sub> barrel domain shares high structural similarity with those of [[GH15]], [[GH37]], [[GH65]], and [[GH94]] <cite>Kurakata2008 Gibson2007</cite>. This similarity had been predicted on the basis of sequence comparison, before their crystal structures were available <cite>Stam2005</cite>. The first crystal structure of the eukaryotic processing &alpha;-glucosidase I ([{{PDBlink}}4j5t PDB 4j5t]) has been reported in 2013 <cite>Barker2013</cite>.<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Human processing &alpha;-glucosidase I <cite>Kalz-Fuller1995</cite>.<br />
;First stereochemistry determination: Processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'' (Cwh41p) <cite>Palcic1999</cite>.<br />
;First general acid residue identification: Inferred from structural comparison <cite>Kurakata2008</cite>.<br />
;First general base residue identification: Inferred from structural comparison <cite>Kurakata2008</cite>.<br />
;First 3-D structure: ''Escherichia coli'' YgjK, an enzyme showing the highest activity for the &alpha;-1,3-glucosidic linkage of nigerose <cite>Kurakata2008</cite>.<br />
;First 3-D structure of a eukaryotic GH63 enzyme: A transmembrane-deleted form of processing &alpha;-glucosidase I from ''Saccharomyces cerevisiae'' <cite>Barker2013</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Alarico2013 pmid=23273275<br />
#Barker2013 pmid=23536181<br />
#Dhanawansa2002 pmid=11971867<br />
#Herscovics1999 pmid=9878780<br />
#Kurakata2008 pmid=18586271<br />
#Palcic1999 pmid=10619707<br />
#Gibson2007 pmid=17455176<br />
#Stam2005 pmid=16226731<br />
#Kalz-Fuller1995 pmid=7635146<br />
<br />
#Miyazaki2013 pmid=23826932<br />
<br />
#Nobre2013 pmid=23179444<br />
<br />
#Alarico2014 pmid=<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH063]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17318User:Takatsugu Miyazaki2023-06-19T03:32:08Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Associate Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]]_16 ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]]_14 ''Pseudopedobacter saltans'' α-galactosidase '''Subfamily First''' <cite>Miyazaki2015a</cite><br />
<br />
*[[GH31]]_15 ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase '''Subfamily First''' <cite>Ikegaya2022</cite><br />
<br />
*[[GH31]]_18 ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase '''Subfamily First''' <cite>Miyazaki2020b Miyazaki2022a</cite><br />
<br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021 Nakamura2023</cite><br />
<br />
*[[GH66]] ''Flavobacterium johnsoniae'' dextranase <cite>Nakamura2023</cite><br />
<br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
<br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016 Nakamura2023</cite><br />
*[[GH31]]_10 ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
<br />
*[[GH31]]_14 ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
<br />
*[[GH31]]_15 ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
<br />
*[[GH31]]_18 ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
<br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
<br />
#Nakamura2023 pmid=37269952<br />
<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17253User:Takatsugu Miyazaki2023-05-01T10:56:33Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Associate Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]]_16 ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]]_14 ''Pseudopedobacter saltans'' α-galactosidase '''Subfamily First''' <cite>Miyazaki2015a</cite><br />
<br />
*[[GH31]]_15 ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase '''Subfamily First''' <cite>Ikegaya2022</cite><br />
<br />
*[[GH31]]_18 ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase '''Subfamily First''' <cite>Miyazaki2020b Miyazaki2022a</cite><br />
<br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021</cite><br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016</cite><br />
*[[GH31]]_10 ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
<br />
*[[GH31]]_14 ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
<br />
*[[GH31]]_15 ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
<br />
*[[GH31]]_18 ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
<br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17252User:Takatsugu Miyazaki2023-05-01T10:55:04Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Associate Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]]_16 ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]]_14 ''Pseudopedobacter saltans'' α-galactosidase <cite>Miyazaki2015a</cite><br />
<br />
*[[GH31]]_15 ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
<br />
*[[GH31]]_18 ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Miyazaki2020b Miyazaki2022a</cite><br />
<br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021</cite><br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016</cite><br />
*[[GH31]]_10 ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
<br />
*[[GH31]]_14 ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
<br />
*[[GH31]]_15 ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
<br />
*[[GH31]]_18 ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
<br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17251User:Takatsugu Miyazaki2023-05-01T10:45:25Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Associate Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]] ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]] ''Pseudopedobacter saltans'' α-galactosidase <cite>Miyazaki2015a</cite><br />
*[[GH31]] ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Miyazaki2020b Miyazaki2022a</cite><br />
*[[GH31]] ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021</cite><br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016</cite><br />
*[[GH31]] ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
*[[GH31]] ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
*[[GH31]] ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_49&diff=17193Glycoside Hydrolase Family 492023-04-14T03:08:30Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH49'''<br />
|-<br />
|'''Clan''' <br />
|GH-N<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH49.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of family 49 cleave &alpha;-1,6-glucosidic linkages or &alpha;-1,4-glucosidic linkages of polysaccharides containing &alpha;-1,6-glucosidic linkages, dextran and pullulan. The major activities reported for this family of glycoside hydrolases are dextranase (EC [{{EClink}}3.2.1.11 3.2.1.11]), and a dextranase from ''Talaromyces minioluteum'' (formerly known as ''Penicillium minioluteum''), Dex49A, is currently the most characterized enzyme. Dextran 1,6-&alpha;-isomaltotriosidase (EC [{{EClink}}3.2.1.95 3.2.1.95]) <cite>Mizuno1999</cite>, isopullulanase (EC [{{EClink}}3.2.1.57 3.2.1.57]) <cite>Sakano1971</cite>, endo-acting sulfated-arabinan hydrolase (EC 3.2.1-) <cite>Helbert2019</cite>, and 4-''O''-α-D-isomaltooligosaccharylmaltooligosaccharide 1,4-α-isomaltooligosaccharohydrolase (EC 3.2.1.-) <cite>Kitagawa2023</cite> have also been described.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH49 &alpha;-glycosidases are [[inverting]] enzymes, as first shown by NMR on a dextranase Dex49A from ''Talaromyces minioluteum'' <cite>Larsson2003</cite> .<br />
<br />
== Catalytic Residues ==<br />
Three Asp residues (Asp376, Asp395, and Asp396 in Dex49A) are conserved in the catalytic centre of members of clan GH-N, GH49 and [[GH28]] enzymes <cite>Larsson2003 Mizuno2008</cite>, and all three of the Asp mutants of a GH49 enzyme, isopullulanase, lost their activities <cite>Akeboshi2004</cite>. The [[general acid]] was first identified in Dex49A from ''Talaromyces minioluteum'' as Asp395 following the three-dimensional structure determination. To date, it is unclear whether either (or both) of the Asp residues (Asp376 and Asp396 in Dex49A) acts as a [[general base]] in the reaction of GH49 and [[GH28]] enzymes <cite>Larsson2003 vanSanten1999 Shimizu2002</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Two structures of GH49 enzymes are available so far <cite>Larsson2003 Mizuno2008</cite>, and they display a two domain structure. The N-terminal domain is a &beta;-sandwich and the C-terminal domain adopts a right-handed parallel &beta;-helix. The similarity of the &beta;-helix fold between GH49 and [[GH28]] enzymes has been described, although almost none of the amino acid residues other than the three catalytic Asp residues is conserved between the two families <cite>Larsson2003 Mizuno2008</cite>. Each coil forming the cylindrical &beta;-helix fold is composed of three &beta;-sheets, which are named PB1, PB2, and PB3, following the original definition for a PL1 enzyme, pectate lyase C <cite>Yoder1993</cite>.<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Dextranase from ''Arthrobacter'' sp. CB-8 <cite>Okushima1991</cite>.<br />
;First sterochemistry determination: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First general acid residue identification: Dextranase (Dex49A) from ''Talaromyces minioluteum'' <cite>Larsson2003</cite>.<br />
;First 3-D structure: Dextranase (Dex49A) from ''Talaromyces minioluteum'' by X-ray crystallography (PDB ID [{{PDBlink}}1ogm 1ogm]) <cite>Larsson2003</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mizuno1999 pmid=10540747<br />
#Larsson2003 pmid=12962629<br />
#Mizuno2008 pmid=18155243<br />
#Akeboshi2004 pmid=15560783<br />
#vanSanten1999 pmid=10521427<br />
#Shimizu2002 pmid=12022868<br />
#Yoder1993 pmid=8502994<br />
#Okushima1991 pmid=1859672<br />
#Sakano1971 Sakano Y, Masuda N, and Kobayashi T. (1971). ''Hydrolysis of Pullulan by a Novel Enzyme from Aspergillus niger'', ''Agric Biol Chem'' 1971;35(6):971-973. https://doi.org/10.1271/bbb1961.35.971<br />
#Helbert2019 pmid=30850540<br />
<br />
#Kitagawa2023 pmid=36592961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH049]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_49&diff=17192Glycoside Hydrolase Family 492023-04-14T03:05:21Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH49'''<br />
|-<br />
|'''Clan''' <br />
|GH-N<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH49.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of family 49 cleave &alpha;-1,6-glucosidic linkages or &alpha;-1,4-glucosidic linkages of polysaccharides containing &alpha;-1,6-glucosidic linkages, dextran and pullulan. The major activities reported for this family of glycoside hydrolases are dextranase (EC [{{EClink}}3.2.1.11 3.2.1.11]), and a dextranase from ''Talaromyces minioluteum'' (formerly known as ''Penicillium minioluteum''), Dex49A, is currently the most characterized enzyme. Dextran 1,6-&alpha;-isomaltotriosidase (EC [{{EClink}}3.2.1.95 3.2.1.95]) <cite>Mizuno1999</cite>, isopullulanase (EC [{{EClink}}3.2.1.57 3.2.1.57]) <cite>Sakano1971</cite>, endo-acting sulfated-arabinan hydrolase (EC 3.2.1-) <cite>Helbert2019</cite>, and 4-''O''-α-D-isomaltooligosaccharylmaltooligosaccharide 1,4-α-isomaltooligosaccharohydrolase (EC 3.2.1.-) <cite>Kitagawa2023</cite> have also been described.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH49 &alpha;-glycosidases are [[inverting]] enzymes, as first shown by NMR on a dextranase Dex49A from ''Penicillium minioluteum'' <cite>Larsson2003</cite> .<br />
<br />
== Catalytic Residues ==<br />
Three Asp residues (Asp376, Asp395, and Asp396 in Dex49A) are conserved in the catalytic centre of members of clan GH-N, GH49 and [[GH28]] enzymes <cite>Larsson2003 Mizuno2008</cite>, and all three of the Asp mutants of a GH49 enzyme, isopullulanase, lost their activities <cite>Akeboshi2004</cite>. The [[general acid]] was first identified in Dex49A from ''Penicillium minioluteum'' as Asp395 following the three-dimensional structure determination. To date, it is unclear whether either (or both) of the Asp residues (Asp376 and Asp396 in Dex49A) acts as a [[general base]] in the reaction of GH49 and [[GH28]] enzymes <cite>Larsson2003 vanSanten1999 Shimizu2002</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Two structures of GH49 enzymes are available so far <cite>Larsson2003 Mizuno2008</cite>, and they display a two domain structure. The N-terminal domain is a &beta;-sandwich and the C-terminal domain adopts a right-handed parallel &beta;-helix. The similarity of the &beta;-helix fold between GH49 and [[GH28]] enzymes has been described, although almost none of the amino acid residues other than the three catalytic Asp residues is conserved between the two families <cite>Larsson2003 Mizuno2008</cite>. Each coil forming the cylindrical &beta;-helix fold is composed of three &beta;-sheets, which are named PB1, PB2, and PB3, following the original definition for a PL1 enzyme, pectate lyase C <cite>Yoder1993</cite>.<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Dextranase from ''Arthrobacter'' sp. CB-8 <cite>Okushima1991</cite>.<br />
;First sterochemistry determination: Dextranase (Dex49A) from ''Penicillium minioluteum'' <cite>Larsson2003</cite>.<br />
;First general acid residue identification: Dextranase (Dex49A) from ''Penicillium minioluteum'' <cite>Larsson2003</cite>.<br />
;First 3-D structure: Dextranase (Dex49A) from ''Penicillium minioluteum'' by X-ray crystallography (PDB ID [{{PDBlink}}1ogm 1ogm]) <cite>Larsson2003</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mizuno1999 pmid=10540747<br />
#Larsson2003 pmid=12962629<br />
#Mizuno2008 pmid=18155243<br />
#Akeboshi2004 pmid=15560783<br />
#vanSanten1999 pmid=10521427<br />
#Shimizu2002 pmid=12022868<br />
#Yoder1993 pmid=8502994<br />
#Okushima1991 pmid=1859672<br />
#Sakano1971 Sakano Y, Masuda N, and Kobayashi T. (1971). ''Hydrolysis of Pullulan by a Novel Enzyme from Aspergillus niger'', ''Agric Biol Chem'' 1971;35(6):971-973. https://doi.org/10.1271/bbb1961.35.971<br />
#Helbert2019 pmid=30850540<br />
<br />
#Kitagawa2023 pmid=36592961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH049]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17182User:Takatsugu Miyazaki2023-04-13T08:13:03Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Assistant Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]] ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]] ''Pseudopedobacter saltans'' α-galactosidase <cite>Miyazaki2015a</cite><br />
*[[GH31]] ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Miyazaki2020b Miyazaki2022a</cite><br />
*[[GH31]] ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021</cite><br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016</cite><br />
*[[GH31]] ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
*[[GH31]] ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
*[[GH31]] ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b pmid=37033117<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_49&diff=17181Glycoside Hydrolase Family 492023-04-13T08:00:20Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takashi Tonozuka|Takashi Tonozuka]] and [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takashi Tonozuka|Takashi Tonozuka]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH49'''<br />
|-<br />
|'''Clan''' <br />
|GH-N<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH49.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of family 49 cleave &alpha;-1,6-glucosidic linkages or &alpha;-1,4-glucosidic linkages of polysaccharides containing &alpha;-1,6-glucosidic linkages, dextran and pullulan. The major activities reported for this family of glycoside hydrolases are dextranase (EC [{{EClink}}3.2.1.11 3.2.1.11]), and a dextranase from ''Talaromyces minioluteum'' (formerly known as ''Penicillium minioluteum''), Dex49A, is currently the most characterized enzyme. Dextran 1,6-&alpha;-isomaltotriosidase (EC [{{EClink}}3.2.1.95 3.2.1.95]) <cite>Mizuno1999</cite>, isopullulanase (EC [{{EClink}}3.2.1.57 3.2.1.57]) <cite>Sakano1971</cite>, endo-acting sulfated-arabinan hydrolase (EC 3.2.1-) <cite>Helbert2019</cite>, and 4-O-α-D-isomaltooligosaccharylmaltooligosaccharide 1,4-α-isomaltooligosaccharohydrolase (EC 3.2.1.-) <cite>Kitagawa2023</cite> have also been described.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH49 &alpha;-glycosidases are [[inverting]] enzymes, as first shown by NMR on a dextranase Dex49A from ''Penicillium minioluteum'' <cite>Larsson2003</cite> .<br />
<br />
== Catalytic Residues ==<br />
Three Asp residues (Asp376, Asp395, and Asp396 in Dex49A) are conserved in the catalytic centre of members of clan GH-N, GH49 and [[GH28]] enzymes <cite>Larsson2003 Mizuno2008</cite>, and all three of the Asp mutants of a GH49 enzyme, isopullulanase, lost their activities <cite>Akeboshi2004</cite>. The [[general acid]] was first identified in Dex49A from ''Penicillium minioluteum'' as Asp395 following the three-dimensional structure determination. To date, it is unclear whether either (or both) of the Asp residues (Asp376 and Asp396 in Dex49A) acts as a [[general base]] in the reaction of GH49 and [[GH28]] enzymes <cite>Larsson2003 vanSanten1999 Shimizu2002</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Two structures of GH49 enzymes are available so far <cite>Larsson2003 Mizuno2008</cite>, and they display a two domain structure. The N-terminal domain is a &beta;-sandwich and the C-terminal domain adopts a right-handed parallel &beta;-helix. The similarity of the &beta;-helix fold between GH49 and [[GH28]] enzymes has been described, although almost none of the amino acid residues other than the three catalytic Asp residues is conserved between the two families <cite>Larsson2003 Mizuno2008</cite>. Each coil forming the cylindrical &beta;-helix fold is composed of three &beta;-sheets, which are named PB1, PB2, and PB3, following the original definition for a PL1 enzyme, pectate lyase C <cite>Yoder1993</cite>.<br />
<br />
== Family Firsts ==<br />
;First gene cloning: Dextranase from ''Arthrobacter'' sp. CB-8 <cite>Okushima1991</cite>.<br />
;First sterochemistry determination: Dextranase (Dex49A) from ''Penicillium minioluteum'' <cite>Larsson2003</cite>.<br />
;First general acid residue identification: Dextranase (Dex49A) from ''Penicillium minioluteum'' <cite>Larsson2003</cite>.<br />
;First 3-D structure: Dextranase (Dex49A) from ''Penicillium minioluteum'' by X-ray crystallography (PDB ID [{{PDBlink}}1ogm 1ogm]) <cite>Larsson2003</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mizuno1999 pmid=10540747<br />
#Larsson2003 pmid=12962629<br />
#Mizuno2008 pmid=18155243<br />
#Akeboshi2004 pmid=15560783<br />
#vanSanten1999 pmid=10521427<br />
#Shimizu2002 pmid=12022868<br />
#Yoder1993 pmid=8502994<br />
#Okushima1991 pmid=1859672<br />
#Sakano1971 Sakano Y, Masuda N, and Kobayashi T. (1971). ''Hydrolysis of Pullulan by a Novel Enzyme from Aspergillus niger'', ''Agric Biol Chem'' 1971;35(6):971-973. https://doi.org/10.1271/bbb1961.35.971<br />
#Helbert2019 pmid=30850540<br />
<br />
#Kitagawa2023 pmid=36592961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH049]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17178Carbohydrate Binding Module Family 942023-04-13T07:26:32Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC [{{EClink}}2.4.1.145 2.4.1.145], Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine (GlcNAc), ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAc-β-(1→2)-Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, GnT-IVa CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 proteins adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|600px|center|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
<br />
== Functionalities == <br />
<br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of mouse GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to the glycan binding function <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17167Carbohydrate Binding Module Family 942023-04-13T06:01:42Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC [{{EClink}}2.4.1.145 2.4.1.145], Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine (GlcNAc), ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAc-β-(1→2)-Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, GnT-IVa CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|300px|right|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 proteins adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of mouse GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to the glycan binding function <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17160Carbohydrate Binding Module Family 942023-04-13T05:44:57Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145, Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine (GlcNAc), ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAc-β-(1→2)-Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, GnT-IVa CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|300px|right|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 proteins adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of mouse GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to the glycan binding function <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17159Carbohydrate Binding Module Family 942023-04-13T05:10:33Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145, Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine (GlcNAc), ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAc-β-(1→2)-Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, GnT-IVa CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|300px|right|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of mouse GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to the glycan binding function <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17158Carbohydrate Binding Module Family 942023-04-13T04:50:17Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145, Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAc-β-(1→2)-Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, GnT-IVa CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|300px|right|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of mouse GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to the glycan binding function <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17157Carbohydrate Binding Module Family 942023-04-13T04:47:55Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145, Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAc-β-(1→2)-Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, GnT-IVa CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|300px|right|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of mouse GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to the glycan binding function <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=File:Fig2_CBM94_structures.png&diff=17156File:Fig2 CBM94 structures.png2023-04-13T04:46:22Z<p>Takatsugu Miyazaki: Takatsugu Miyazaki uploaded a new version of File:Fig2 CBM94 structures.png</p>
<hr />
<div></div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17155Carbohydrate Binding Module Family 942023-04-13T04:43:26Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145, Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAc-β-(1→2)-Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|300px|right|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of mouse GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to the glycan binding function <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17154Carbohydrate Binding Module Family 942023-04-13T04:41:04Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145, Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAc-β-(1→2)-Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|300px|right|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of mouse GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to glycan binding <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17153Carbohydrate Binding Module Family 942023-04-13T04:36:59Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145, Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAc-β-(1→2)-Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|300px|right|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of murine GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to glycan binding <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17152Carbohydrate Binding Module Family 942023-04-13T04:35:58Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145, Fig. 1) and an ortholog from lepidopteran insect ''Bombyx mori'' (silkworm) <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans to substrate ''N''-glycans (Fig. 1).<br />
== Structural Features ==<br />
<br />
[[File:Fig2 CBM94 structures.png|thumb|300px|right|'''Figure 2. Overall structures of CBM94 proteins.''' (Left to right) Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT], human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL], and ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. ]]<br />
<br />
[[File:Fig3 CBM94 bindingsite.png|thumb|300px|right|'''Figure 3. GlcNAc-binding sites of CBM94 proteins.''' Mouse GnT-IVa CBM94 (D445A mutant) [{{PDBlink}}7VMT 7VMT] and human GnT-IVa CBM94 [{{PDBlink}}7XTL 7XTL] are superimposed into ''B. mori'' GnT-IV ortholog CBM94 in complex with GlcNAc (''magenta'' stick) [{{PDBlink}}7XTN 7XTN]. Amino acid residues interacting with GlcNAc in ''B. mori'' CBM94 and the corresponding residues in human and mouse CBM94 are represented as stick models.]]<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix (Fig. 2). They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding (Fig. 3). These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of murine GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to glycan binding <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17151Carbohydrate Binding Module Family 942023-04-13T03:21:32Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
[[File:Fig1 GnTIV reaction.png|thumb|300px|right|'''Figure 1. Reaction catalyzed by GnT-IVa and GnT-IVb.''' [[GT54]] GnT-IVa and GnT-IVb transfer GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,3 arm, while GnT-IVc (also known as GnT-VI) transfers GlcNAc to β-1,2-GlcNAc-attached mannose residue of α-1,6 arm in ''N''-glycans. ]]<br />
<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans to substrate ''N''-glycans.<br />
== Structural Features ==<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix. They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding. These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of murine GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to glycan binding <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=File:Fig3_CBM94_bindingsite.png&diff=17150File:Fig3 CBM94 bindingsite.png2023-04-13T03:10:45Z<p>Takatsugu Miyazaki: </p>
<hr />
<div></div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=File:Fig2_CBM94_structures.png&diff=17149File:Fig2 CBM94 structures.png2023-04-13T03:10:19Z<p>Takatsugu Miyazaki: </p>
<hr />
<div></div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=File:Fig1_GnTIV_reaction.png&diff=17148File:Fig1 GnTIV reaction.png2023-04-13T03:09:22Z<p>Takatsugu Miyazaki: </p>
<hr />
<div></div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17147Carbohydrate Binding Module Family 942023-04-13T00:51:02Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed lower affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans to substrate ''N''-glycans.<br />
<br />
== Structural Features ==<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix. They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding [[CBM32]] domain (NagHCBM32-2) of ''Clostridium perfringens'' [[GH84]] β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding. These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of murine GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to glycan binding <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17146Carbohydrate Binding Module Family 942023-04-12T16:07:37Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed low affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans rather than substrate ''N''-glycans.<br />
<br />
== Structural Features ==<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix. They are structurally homologous to CBM32 proteins, such as a GlcNAc-binding CBM32 domain (NagHCBM32-2) of ''Clostridium perfringens'' GH84 β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding. These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of murine GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to glycan binding <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17145Carbohydrate Binding Module Family 942023-04-12T16:06:08Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed low affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans rather than substrate ''N''-glycans.<br />
<br />
== Structural Features ==<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix. They are structurally homologous to CBM32 proteins, such as GlcNAc-binding CBM32 domain (NagHCBM32-2) of ''Clostridium perfringens'' GH84 β-''N''-acetylglucosaminidase NagH <cite>Ficko-Blean2009</cite>. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding. These residues are completely conserved among NagHCBM32-2 and CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to sugars, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced the glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. A comparative study of murine GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to glycan binding <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
#Ficko-Blean2009 pmid=19422833<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17139Carbohydrate Binding Module Family 942023-04-12T11:47:48Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed low affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans rather than substrate ''N''-glycans.<br />
<br />
== Structural Features ==<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix. They are structurally homologous to CBM32 proteins, such as GlcNAc-binding CBM32 domain of ''Clostridium perfringens'' GH84 β-''N''-acetylglucosaminidase NagH. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding. These residues are completely conserved among CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
<br />
== Functionalities == <br />
The CBM94 domains of human GnT-IVa and ''B. mori'' ortholog were only examined for affinity to GlcNAc and ligands containing a β-GlcNAc residue, but the CBM94 domain of mouse GnT-IVa was examined for its relevance to enzyme activity and substrate specificity. The deletion of the CBM94 domain markedly reduced the activity of mouse GnT-IVa, and the replacement of Asp445, which binds GlcNAc, with Ala also reduced glycosyltransferase activity. Based on its affinity for glycans, it is possible that the function of the CBM94 domain is to regulate the catalytic cycle from enzymatic reaction to product release rather than to capture substrates <cite>Nagae2022</cite>. The comparative study of murine GnT-IVa and GnT-IVb suggested that their CBM94 domains affect substrate glycoprotein preference in addition to glycan binding <cite>Osada2022</cite>. It should be noted that a CBM94 domain is conserved among GnT-IV isozymes, GnT-IVa, -IVb, and -IVc, but is completely absent in GnT-IVd (MGAT4D), which has no enzymatic activity observed and inhibits GnT-I activity <cite>Huang2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
#Huang2015 pmid=26371870<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=User:Takatsugu_Miyazaki&diff=17070User:Takatsugu Miyazaki2023-02-04T07:15:06Z<p>Takatsugu Miyazaki: </p>
<hr />
<div>[[Image:Takatsugu_Miyazaki.png|right]]<br />
Takatsugu Miyazaki is an Assistant Professor of [https://green.shizuoka.ac.jp/en/ Research Institute of Green Science and Technology] (RIGST) and [https://www.agr.shizuoka.ac.jp/en/ Department of Agriculture, Graduate School of Integrated Science and Technology], at [https://www.shizuoka.ac.jp/english/ Shizuoka University]. He obtained his PhD under the supervision of [[User:Takashi Tonozuka|Takashi Tonozuka]] at Tokyo University of Agriculture and Technology. He is interested in structures and functions of CAZymes, especially glycoside hydrolases and glycosyltransferases from microorganisms and insects. He has contributed to the crystal structure determination of<br />
<br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6C <cite>Liu2010</cite><br />
*[[GH6]] ''Coprinopsis cinerea'' cellobiohydrolase CcCel6A <cite>Tamura2012</cite><br />
*[[GH13]]_17 ''Bombyx mori'' sucrose hydrolase BmSUH <cite>Miyazaki2020a</cite><br />
*[[GH16]] ''Microbulbifer thermotolerans'' β-agarase <cite>Takagi2015</cite><br />
*[[GH27]] ''Arthrobacter globiformis'' isomalto-dextranase <cite>Okazawa2015</cite><br />
*[[GH31]] ''Pseudopedobacter saltans'' α-galactosidase <cite>Miyazaki2015a</cite><br />
*[[GH31]] ''Enterococcus faecalis'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Miyazaki2020b Miyazaki2022a</cite><br />
*[[GH31]] ''Lactococcus lactis'' subsp. ''cremoris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
*[[GH32]] ''Bombyx mori'' β-fructofuranosidase BmSUC1 <cite>Miyazaki2020c</cite><br />
*[[GH49]] ''Aspergillus brasiliensis'' isopullulanase (''N''-glycan-deficient variant) <cite>Miyazaki2015b</cite><br />
*[[GH62]] ''Coprinopsis cinerea'' α-L-arabinofuranosidase CcAbf62A <cite>Tonozuka2017</cite><br />
*[[GH63]] ''Escherichia coli'' α-glycosidase YgjK (glycosynthase mutant) <cite>Miyazaki2013a Miyazaki2016</cite><br />
*[[GH63]] ''Thermus thermophillus'' mannosylglycerate hydrolase <cite>Miyazaki2015c</cite><br />
*[[GH65]] ''Flavobacterium johnsoniae'' kojibiose hydrolase <cite>Nakamura2021</cite><br />
*[[GH68]] ''Microbacterium saccharophilum'' β-fructofuranosidase <cite>Tonozuka2012</cite> and its thermostabilized mutants <cite>Ohta2014</cite><br />
*[[GH92]] ''Enterococcus faecalis'' α-1,2-mannosidase (Michaelis complex) <cite>Alonso-Gil2022</cite><br />
*[[GH131]] ''Coprinopsis cinerea'' CcGH131A '''Family First''' <cite>Miyazaki2013b</cite><br />
<br />
*[[CBM94]] C-terminal domains of ''Homo sapiens'' [[GT54]] ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A) and ''Bombyx mori'' ortholog '''Family First''' <cite>Oka2022</cite><br />
<br />
<br />
He also has contributed to identification and characterization of<br />
<br />
*[[GH29]] ''Bombyx mori'' α-L-fucosidase <cite>Nakamura2020</cite><br />
*[[GH31]] ''Pedobacter heparinus'' α-galactosidase <cite>Miyazaki2015a</cite><br />
*[[GH31]] ''Flavobacterium johnsoniae'' dextranase <cite>Gozu2016</cite><br />
*[[GH31]] ''Paenibacillus'' sp. 598K 6-α-glucosyltransferase <cite>Ichinose2017</cite><br />
*[[GH31]] ''Bombyx mori'' exo-acting protein-α-''N''-acetylgalactosaminidase <cite>Ikegaya2021</cite><br />
*[[GH31]] ''Cordyceps militaris'' α-1,3-glucosidase <cite>Ikegaya2022</cite><br />
*[[GH63]] ''Aspergillus brasiliensis'' mannosyl-oligosaccharide glucosidase <cite>Miyazaki2011</cite><br />
*[[GH65]] ''Microbacterium dextranolyticum'' dextran α-1,2-debranching enzyme <cite>Miyazaki2022b</cite><br />
*[[GH66]] ''Paenibacillus'' sp. 598K dextranase <cite>Mizushima2019</cite><br />
*[[GH99]] ''Shewanella amazonensis'' endo-α-1,2-mannosidase <cite>Matsuda2011</cite><br />
<br />
*[[GT7]] ''Bombyx mori'' β-1,4-''N''-acetylgalactosaminyltransferase <cite>Miyazaki2019a</cite><br />
*[[GT16]] ''Homo sapiens'' β-1,2-''N''-acetylglucosaminyltransferase II recombinantly expressed in ''Bombyx mori'' <cite>Miyazaki2018</cite><br />
*[[GT16]] ''Bombyx mori'' β-1,2-''N''-acetylglucosaminyltransferase II <cite>Miyazaki2019b</cite><br />
<br />
*[[PL21]] ''Pedobacter heparinus'' heparin lyase II (mutants) <cite>Mori2016</cite><br />
----<br />
<br />
<biblio><br />
#Liu2010 pmid=20148970<br />
#Tamura2012 pmid=22429290<br />
#Miyazaki2020a pmid=32381508<br />
#Takagi2015 pmid=25483365<br />
#Okazawa2015 pmid=26330557<br />
#Miyazaki2015a pmid=25942325<br />
#Miyazaki2020b pmid=32367553<br />
#Miyazaki2022a pmid=34826537<br />
#Ikegaya2022 pmid=35293315<br />
#Miyazaki2020c pmid=33132139<br />
#Miyazaki2015b pmid=25359784<br />
#Tonozuka2017 pmid=27589854<br />
#Miyazaki2013a pmid=23826932<br />
#Miyazaki2016 pmid=27688023<br />
#Miyazaki2015c pmid=25712767<br />
#Nakamura2021 pmid=34728215<br />
#Tonozuka2012 pmid=23040392<br />
#Ohta2014 pmid=24633372<br />
#Alonso-Gil2022 pmid=35049087<br />
#Miyazaki2013b pmid=23711369<br />
#Oka2022 pmid=36106687<br />
#Nakamura2020 pmid=32561391<br />
#Gozu2016 pmid=27170214<br />
#Ichinose2017 pmid=28224195<br />
#Ikegaya2021 pmid=33742736<br />
#Miyazaki2011 pmid=22020441<br />
#Miyazaki2022b Miyazaki T, Tanaka H, Nakamura S, Dohra H, and Funane K. (2022). ''Identification and Characterization of Dextran α-1,2-Debranching Enzyme from Microbacterium dextranolyticum'', ''J Appl Glycosci'' in press. https://doi.org/10.5458/jag.jag.JAG-2022_0013<br />
#Mizushima2019 pmid=31273396<br />
#Matsuda2011 pmid=21512220<br />
#Miyazaki2019a pmid=31655162<br />
#Miyazaki2018 pmid=29409697<br />
#Miyazaki2019b pmid=30253927<br />
#Mori2016 pmid=34354475<br />
<br />
</biblio><br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Miyazaki,Takatsugu]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17023Carbohydrate Binding Module Family 942023-01-20T08:13:52Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed low affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans rather than substrate ''N''-glycans.<br />
<br />
== Structural Features ==<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB ID [{{PDBlink}}7XTL 7XTL], [{{PDBlink}}7VMT 7VMT], and [{{PDBlink}}7XTM 7XTM]), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix. They are structurally homologous to CBM32 proteins, such as GlcNAc-binding CBM32 domain of ''Clostridium perfringens'' GH84 β-''N''-acetylglucosaminidase NagH. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc (PDB ID [{{PDBlink}}7XTN 7XTN]) indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding. These residues are completely conserved among CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
<br />
== Functionalities == <br />
''Content in this section should include, in paragraph form, a description of:''<br />
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.<br />
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)<br />
* '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17022Carbohydrate Binding Module Family 942023-01-20T08:08:37Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed low affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans rather than substrate ''N''-glycans.<br />
<br />
== Structural Features ==<br />
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB 7XTL, 7VMT, and 7XTM), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix. They are structurally homologous to CBM32 proteins, such as GlcNAc-binding CBM32 domain of ''Clostridium perfringens'' GH84 β-''N''-acetylglucosaminidase NagH. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding. These residues are completely conserved among CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.<br />
<br />
== Functionalities == <br />
''Content in this section should include, in paragraph form, a description of:''<br />
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.<br />
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)<br />
* '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17021Carbohydrate Binding Module Family 942023-01-20T05:06:05Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed low affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans rather than substrate ''N''-glycans.<br />
<br />
== Structural Features ==<br />
''Content in this section should include, in paragraph form, a description of:''<br />
* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)<br />
* '''Type:''' Include here Type A, B, or C and properties<br />
* '''Features of ligand binding:''' Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.<br />
<br />
== Functionalities == <br />
''Content in this section should include, in paragraph form, a description of:''<br />
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.<br />
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)<br />
* '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17020Carbohydrate Binding Module Family 942023-01-20T03:26:17Z<p>Takatsugu Miyazaki: Undo revision 17019 by Takatsugu Miyazaki (talk)</p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' comprise of around 140 amino acid residues and showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed low affinity for ''N''-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans rather than substrate ''N''-glycans.<br />
<br />
== Structural Features ==<br />
''Content in this section should include, in paragraph form, a description of:''<br />
* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)<br />
* '''Type:''' Include here Type A, B, or C and properties<br />
* '''Features of ligand binding:''' Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.<br />
<br />
== Functionalities == <br />
''Content in this section should include, in paragraph form, a description of:''<br />
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.<br />
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)<br />
* '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazakihttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_94&diff=17019Carbohydrate Binding Module Family 942023-01-20T03:25:27Z<p>Takatsugu Miyazaki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
* [[Responsible Curator]]: [[User:Takatsugu Miyazaki|Takatsugu Miyazaki]]<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM94.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human ''N''-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; [[GT54]]; EC 2.4.1.145) and an ortholog from lepidopteran insect ''Bombyx mori'' <cite>Oka2022</cite>. The CBM94 proteins from human and ''B. mori'' comprise of around 140 amino acid residues and showed affinity toward ''N''-acetylglucosamine, ''N'',''N''’-diacetylchitobiose, and ''p''-nitrophenyl β-''N''-acetylglucosaminide with ''K''<sub>a</sub> values of 242–1,970 M<sup>−1</sup>. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and ''N''-acetylgalactosamine, some of which are components of matured ''N''-glycans <cite>Oka2022</cite>. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis <cite>Nagae2022</cite>. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for ''N''-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed low affinity for ''N''-glycan with only β-(1→2)-capped GlcNAc, which is the substrate of GnT-IV <cite>Nagae2022</cite>. Therefore, CBM94 prefers product ''N''-glycans rather than substrate ''N''-glycans.<br />
<br />
== Structural Features ==<br />
''Content in this section should include, in paragraph form, a description of:''<br />
* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)<br />
* '''Type:''' Include here Type A, B, or C and properties<br />
* '''Features of ligand binding:''' Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.<br />
<br />
== Functionalities == <br />
''Content in this section should include, in paragraph form, a description of:''<br />
* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.<br />
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)<br />
* '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.<br />
<br />
== Family Firsts ==<br />
;First Identified<br />
:Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog was identified independently by two groups <cite>Oka2022,Nagae2022</cite>. <br />
;First Structural Characterization<br />
:Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and ''Bombyx mori'' ortholog were determined independently by two groups <cite>Oka2022,Nagae2022</cite>. β-GlcNAc-bound structure of ''B. mori'' CBM94 was also determined <cite>Oka2022</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Oka2022 pmid=36106687<br />
#Nagae2022 pmid=35854001<br />
#Osada2022 pmid=35988645<br />
<br />
<br />
</biblio><br />
<!-- Do not delete this Category tag --><br />
[[Category:Carbohydrate Binding Module Families|CBM094]]</div>Takatsugu Miyazaki