CAZypedia - User contributions [en-ca]

Glycoside Hydrolase Family 172

2023-09-21T07:39:31Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: [[User:Toma Kashima|Toma Kashima]]
* [[Responsible Curator]]: [[User:Shinya Fushinobu|Shinya Fushinobu]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH172'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH172.html
|}
</div>


== Substrate specificities ==
Glycoside hydrolase family 172 (GH172) includes α-D-arabinofuranosidases and α-D-fructofuranosidases. This family was established following the discovery of αFFase1 from ''Bifidobacterium dentium'' by Kashima et al. in 2021 <cite>Kashima2021</cite>. αFFase1 hydrolyzes the alkylated glycosides Me-α-D-Ara''f'' and Me-α-D-Fru''f''. In nature, it catalyzes the dehydrating condensation reaction of inulobiose (β-D-Fru''f''-(2→1)-α-D-Fru''f'') to difructose dianhydride I (DFA I, α-D-Fru''f''-1,2′:2,1′-β-D-Fru''f''). The dehydrating condensation reaction reaches equilibrium when the ratio of DFA and inulobiose is 9:1. αFFase1 is less specific for D-Fru at the non-reducing end and is able to catalyze the dehydrating condensation of β-D-Fru''p''-(2→1)-α-D-Fru''f'' to diheterolevulosan II (DHL II, α-D-Fru''p''-1,2′:2,1′-β-D-Fru''f''). Physiologically, it is believed that after degradation of DFA I to inulobiose, inulobiose is degraded to D-Fru by [https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_32 GH32] β-D-fructofuranosidase, and then the produced monosaccharides are metabolized by the microorganism. DFA I is an oligosaccharide found in caramel, and since the degradation system of DFA I by bifidobacteria has been clarified, DFA I has attracted a certain attention in the food industry.

Also, some GH172 enzymes which physiologically functions as α-D-arabinofuranosidase, was reported in 2023 by Al-Jourani et al. (DgGH172a, DgGH172b, DgGH172c <cite>Al-Jourani2023</cite>) and Shimokawa et al. (ExoMA1 <cite>Shimokawa2023</cite>). In particular, ExoMA1 was compared in detail with αFFase1, and it was found that its α-D-fructofuranosidase activity is extremely weak. These enzymes are believed to be involved in the degradation system of D-arabinan in the cell walls of Mycobacteria and other acid-fast bacteria, and are expected to be applied to the development of therapeutic, preventive, and diagnostic agents for infectious diseases.

== Kinetics and Mechanism ==
[[File:GH172 aFFase1 mechanism.jpg|thumb|300px|right|'''Figure 1.''' The catalytic mechanism of Inulobiose dehydration by αFFase1.]]
As of 2023, all of the enzymes reported in GH172 catalyze reactions by an anomer-[https://www.cazypedia.org/index.php/Glycoside_hydrolases#Mechanistic_classification retaining] mechanism. When ''p''NP-D-Ara''f'' is hydrolyzed by αFFase1 <cite>Kashima2021</cite> or ExoMA1 <cite>Shimokawa2023</cite>, the initial product was identified by 1H NMR to have the same anomeric conformation as the substrate. In addition, when ''p''NP-α-D-Ara''f'' was enzymatically treated in the presence of organic solvents, [https://www.cazypedia.org/index.php/Transglycosylases transglycosylation] products were detected by TLC. Enzyme kinetic experiments with this substrate were first reported for αFFase1, with ''K''m and ''k''cat values of 2.71 mM and 127.5 s-1, respectively; kinetic constants for ExoMA1 were comparable.

The dehydrating condensation reaction of inulobiose to DFA I by αFFase1 was proposed to proceed as follows ('''Figure 1''').

(i) The reducing end sugar of inulobiose changes its furanose/pyranose and α/β forms in the internal cavity of αFFase1 as well as in solution because of mutarotation.

(ii) The active site of αFFase1 selectively accommodates the α-furanose form in the −1 subsite. The +1 subsite can also accommodate the pyranose moiety of Frupβ2,1Fru. Glu270 donates a proton (general acid catalysis) to the O2 hydroxy group of α-Fruf at the −1 subsite, and Glu291 works as a nucleophile to the anomeric carbon (C2). After this step, the O2 hydroxy group is released from the substrate as a water molecule.

(iii) Rotations of the glycosidic bond and the C1–C2 bond of the +1-subsite sugar are required for the intramolecular transfer reaction to occur.

(iv) When the C1 hydroxy group of fructose at the +1 subsite is appropriately positioned for proton acceptance (general base catalysis) by Glu270, deglycosylation of Glu291 is facilitated.

(v) After the reaction at the active site, DFA I is released through the channel to the inner cavity of the hexamer of αFFase1.

The opposite reaction from DFA I (v) to inulobiose (i) is expected to be similar to the standard retaining reaction mechanism of GHs. The ''k''cat/''K''m were 0.813 mM-1·s-1 and 0.0378 mM-1·s-1 for inulobiose dehydration and DFA I hydrolysis, respectively.

== Catalytic Residues ==
[[File:GH172 aFFase1 Active Site.png|thumb|300px|right|'''Figure 2.''' The active site of αFFase1.]]
X-ray crystallographic analysis of the catalytic residues of αFFase1 <cite>Kashima2021</cite> and ExoMA1 <cite>Shimokawa2023</cite> revealed that the hydrolysis and dehydrating condensation reactions reported in GH172 are catalyzed by two glutamate residues, which act as the [https://www.cazypedia.org/index.php/Catalytic_nucleophile catalytic nucleophile] and the [https://www.cazypedia.org/index.php/General_acid/base general acid/base]. In particular, site-directed mutagenesis of the two catalytic residues of αFFase1 and the amino acid residues that form the −1 and +1 subsites was performed, and the mode of ligand recognition and catalytic mechanism has been analyzed in detail ('''Figure 2''').

== Three-dimensional structures ==
[[File:GH172 aFFase1 and ExoMA1.png|thumb|300px|right|'''Figure 3.''' The overall structure of αFFase1 ('''A''') and ExoMA1 ('''B''').]]
GH172 has a double jelly-roll (DJR) fold consisting of two β-jelly roll domains in the monomer. This is a fold that had not been reported in CAZymes prior to the establishment of GH172. The basic structure is a ''C''3 symmetrical trimer, and the active site is formed by the first β-jelly roll and the second β-jelly roll of the adjacent subunit. The addition of α-helix or loops to the basic structure enables the elaboration of a higher quaternary structure. For example, in αFFase1, a long C-terminal α-helix covers the outside of the overall structure to maintain a ''D''3 dihedral hexameric structure ('''Figure 3A''' <cite>Kashima2021</cite>), while in ExoMA1, loops in the DJR are elongated to form a tetrahedral dodecamer ('''Figure 3B''' <cite>Shimokawa2023</cite>). A small molecule predicted to be a phosphate is coordinated between the trimers in ExoMA1. In addition, BACUNI_00161, a protein of unknown function which belongs to GH172, forms a hexamer by hooking the C-terminal α-helix between the subunits facing each other. It is possible that various other oligomeric forms exist, suggesting that GH172 is a structurally diverse family.

== Family Firsts ==
;First stereochemistry determination: DFA I synthase/hydrolase αFFase1 from ''Bifidobacterium dentium'' JCM 1195 1H NMR.
;First catalytic nucleophile identification: DFA I synthase/hydrolase αFFase1 from ''Bifidobacterium dentium'' JCM 1195 by X-ray crystallography and site-directed mutagenesis.
;First general acid/base residue identification: DFA I synthase/hydrolase αFFase1 from ''Bifidobacterium dentium'' JCM 1195 by X-ray crystallography and site-directed mutagenesis.
;First 3-D structure: BACUNI_00161 from ''Bacteroides uniformis'' ATCC 8492 by X-ray crystallography. This structure was determined as part of structural genomics, and therefore the function of this enzyme has not been confirmed, although it is expected to be α-D-arabinofuranosidase based on sequence homology. The next one determined was DFA I synthase/hydrolase αFFase1 from ''Bifidobacterium dentium'' JCM 1195 by X-ray crystallography..

== References ==
<biblio>
#Kashima2021 pmid=34688653
#Al-Jourani2023 pmid=37076525
#Shimokawa2023 Shimokawa, M., Ishiwata, A., Kashima, T. et al. (2023) ''Identification and characterization of endo-α-, exo-α-, and exo-β-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria''. ''Nature Communications'' 14, 5803. [https://doi.org/10.1038/s41467-023-41431-2 DOI:10.1038/s41467-023-41431-2]
</biblio>


[[Category:Glycoside Hydrolase Families|GH172]]

Glycoside Hydrolase Family 172

2023-09-21T07:38:29Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: [[User:Toma Kashima|Toma Kashima]]
* [[Responsible Curator]]: [[User:Shinya Fushinobu|Shinya Fushinobu]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH172'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH172.html
|}
</div>


== Substrate specificities ==
Glycoside hydrolase family 172 (GH172) includes α-D-arabinofuranosidases and α-D-fructofuranosidases. This family was established following the discovery of αFFase1 from ''Bifidobacterium dentium'' by Kashima et al. in 2021 <cite>Kashima2021</cite>. αFFase1 hydrolyzes the alkylated glycosides Me-α-D-Ara''f'' and Me-α-D-Fru''f''. In nature, it catalyzes the dehydrating condensation reaction of inulobiose (β-D-Fru''f''-(2→1)-α-D-Fru''f'') to difructose dianhydride I (DFA I, α-D-Fru''f''-1,2′:2,1′-β-D-Fru''f''). The dehydrating condensation reaction reaches equilibrium when the ratio of DFA and inulobiose is 9:1. αFFase1 is less specific for D-Fru at the non-reducing end and is able to catalyze the dehydrating condensation of β-D-Fru''p''-(2→1)-α-D-Fru''f'' to diheterolevulosan II (DHL II, α-D-Fru''p''-1,2′:2,1′-β-D-Fru''f''). Physiologically, it is believed that after degradation of DFA I to inulobiose, inulobiose is degraded to D-Fru by [https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_32 GH32] β-D-fructofuranosidase, and then the produced monosaccharides are metabolized by the microorganism. DFA I is an oligosaccharide found in caramel, and since the degradation system of DFA I by bifidobacteria has been clarified, DFA I has attracted a certain attention in the food industry.

Also, some GH172 enzymes which physiologically functions as α-D-arabinofuranosidase, was reported in 2023 by Al-Jourani et al. (DgGH172a, DgGH172b, DgGH172c <cite>Al-Jourani2023</cite>) and Shimokawa et al. (ExoMA1 <cite>Shimokawa2023</cite>). In particular, ExoMA1 was compared in detail with αFFase1, and it was found that its α-D-fructofuranosidase activity is extremely weak. These enzymes are believed to be involved in the degradation system of D-arabinan in the cell walls of Mycobacteria and other acid-fast bacteria, and are expected to be applied to the development of therapeutic, preventive, and diagnostic agents for infectious diseases.

== Kinetics and Mechanism ==
[[File:GH172 aFFase1 mechanism.jpg|thumb|300px|right|'''Figure 1.''' The catalytic mechanism of Inulobiose dehydration by αFFase1.]]
As of 2023, all of the enzymes reported in GH172 catalyze reactions by an anomer-[https://www.cazypedia.org/index.php/Glycoside_hydrolases#Mechanistic_classification retaining] mechanism. When ''p''NP-D-Ara''f'' is hydrolyzed by αFFase1 <cite>Kashima2021</cite> or ExoMA1 <cite>Shimokawa2023</cite>, the initial product was identified by 1H NMR to have the same anomeric conformation as the substrate. In addition, when ''p''NP-α-D-Ara''f'' was enzymatically treated in the presence of organic solvents, [https://www.cazypedia.org/index.php/Transglycosylases transglycosylation] products were detected by TLC. Enzyme kinetic experiments with this substrate were first reported for αFFase1, with ''K''m and ''k''cat values of 2.71 mM and 127.5 s-1, respectively; kinetic constants for ExoMA1 were comparable.

The dehydrating condensation reaction of inulobiose to DFA I by αFFase1 was proposed to proceed as follows ('''Figure 1''').

(i) The reducing end sugar of inulobiose changes its furanose/pyranose and α/β forms in the internal cavity of αFFase1 as well as in solution because of mutarotation.

(ii) The active site of αFFase1 selectively accommodates the α-furanose form in the −1 subsite. The +1 subsite can also accommodate the pyranose moiety of Frupβ2,1Fru. Glu270 donates a proton (general acid catalysis) to the O2 hydroxy group of α-Fruf at the −1 subsite, and Glu291 works as a nucleophile to the anomeric carbon (C2). After this step, the O2 hydroxy group is released from the substrate as a water molecule.

(iii) Rotations of the glycosidic bond and the C1–C2 bond of the +1-subsite sugar are required for the intramolecular transfer reaction to occur.

(iv) When the C1 hydroxy group of fructose at the +1 subsite is appropriately positioned for proton acceptance (general base catalysis) by Glu270, deglycosylation of Glu291 is facilitated.

(v) After the reaction at the active site, DFA I is released through the channel to the inner cavity of the hexamer of αFFase1.

The opposite reaction from DFA I (v) to inulobiose (i) is expected to be similar to the standard retaining reaction mechanism of GHs. The ''k''cat/''K''m were 0.813 mM-1·s-1 and 0.0378 mM-1·s-1 for inulobiose dehydration and DFA I hydrolysis, respectively.

== Catalytic Residues ==
[[File:GH172 aFFase1 Active Site.png|thumb|300px|right|'''Figure 2.''' The active site of αFFase1.]]
X-ray crystallographic analysis of the catalytic residues of αFFase1 <cite>Kashima2021</cite> and ExoMA1 <cite>Shimokawa2023</cite> revealed that the hydrolysis and dehydrating condensation reactions reported in GH172 are catalyzed by two glutamate residues, which act as the [https://www.cazypedia.org/index.php/Catalytic_nucleophile catalytic nucleophile] and the [https://www.cazypedia.org/index.php/General_acid/base general acid/base]. In particular, site-directed mutagenesis of the two catalytic residues of αFFase1 and the amino acid residues that form the −1 and +1 subsites was performed, and the mode of ligand recognition and catalytic mechanism has been analyzed in detail ('''Figure 2''').

== Three-dimensional structures ==
[[File:GH172 aFFase1 and ExoMA1.png|thumb|300px|right|'''Figure 3.''' The overall structure of αFFase1 ('''A''') and ExoMA1 ('''B''').]]
GH172 has a double jelly-roll (DJR) fold consisting of two β-jelly roll domains in the monomer. This is a fold that had not been reported in CAZymes prior to the establishment of GH172. The basic structure is a ''C''3 symmetrical trimer, and the active site is formed by the first β-jelly roll and the second β-jelly roll of the adjacent subunit. The addition of α-helix or loops to the basic structure enables the elaboration of a higher quaternary structure. For example, in αFFase1, a long C-terminal α-helix covers the outside of the overall structure to maintain a ''D''3 dihedral hexameric structure ('''Figure 3A''' <cite>Kashima2021</cite>), while in ExoMA1, loops in the DJR are elongated to form a tetrahedral dodecamer ('''Figure 3B''' <cite>Shimokawa2023</cite>). A small molecule predicted to be a phosphate is coordinated between the trimers in ExoMA1. In addition, BACUNI_00161, a protein of unknown function which belongs to GH172, forms a hexamer by hooking the C-terminal α-helix between the subunits facing each other. It is possible that various other oligomeric forms exist, suggesting that GH172 is a structurally diverse family.

== Family Firsts ==
;First stereochemistry determination: DFA I synthase/hydrolase αFFase1 from ''Bifidobacterium dentium'' JCM 1195 1H NMR.
;First catalytic nucleophile identification: DFA I synthase/hydrolase αFFase1 from ''Bifidobacterium dentium'' JCM 1195 by X-ray crystallography and site-directed mutagenesis.
;First general acid/base residue identification: DFA I synthase/hydrolase αFFase1 from ''Bifidobacterium dentium'' JCM 1195 by X-ray crystallography and site-directed mutagenesis.
;First 3-D structure: BACUNI_00161 from ''Bacteroides uniformis'' ATCC 8492 by X-ray crystallography. This structure was determined as part of structural genomics, and therefore the function of this enzyme has not been confirmed, although it is expected to be α-D-arabinofuranosidase based on sequence homology. The next one determined was DFA I synthase/hydrolase αFFase1 from ''Bifidobacterium dentium'' JCM 1195 by X-ray crystallography..

== References ==
<biblio>
#Kashima2021 pmid=34688653
#Al-Jourani2023 pmid=37076525
#Shimokawa2023 Shimokawa, M., Ishiwata, A., Kashima, T. et al. (2023) ''Identification and characterization of endo-α-, exo-α-, and exo-β-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria''. ''Nature Communications'' 14, 5803. [https://doi.org/10.1038/s41467-023-41431-2 DOI:10.1038/s41467-023-41431-2]
</biblio>


[[Category:Glycoside Hydrolase Families|GH172]]

Glycoside Hydrolase Family 136

2023-06-23T08:06:58Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: [[User:Chihaya Yamada|Chihaya Yamada]]
* [[Responsible Curator]]: [[User:Shinya Fushinobu|Shinya Fushinobu]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH136'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|Asp
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH136.html
|}
</div>


== Substrate specificities ==
This family of glycoside hydrolases contains lacto-''N''-biosidase, as demonstrated for LnbX from ''Bifidobacterium longum'' JCM 1217 <cite>Sakurama2013</cite>. LnbX liberates Galβ1-3GlcNAc (lacto-''N''-biose I, LNB) and lactose from lacto-''N''-tetraose, the main component of human milk oligosaccharides. It hydrolyzed the linkage GlcNAcβ1-3Gal in lacto-''N''-hexaose, lacto-''N''-fucopentaose I, and sialyllacto-''N''-tetraose a of human milk oligosaccharides as substrate of LnbX in the GH136. In addition, LnbX liberates Galβ1-3GalNAc (GNB) from the sugar chains of globo- and ganglio-series glycosphingolipids <cite>Gotoh2015</cite>.

Majority of GH136 lacto-''N''-biosidases require a neighboring chaperon gene for folding. Rarely, chaperone-like gene is fused to lacto-''N''-biosidase gene in case of ErLnb136I and ErLnb136II from ''Eubacterium ramulus'' <cite>Michael2020</cite>.

== Kinetics and Mechanism ==
GH136 lacto-''N''-biosidases hydrolyze the glycosidic linkage via anomer-retaining mechanism. The acid/base catalytic residue of LnbX (Asp411) formed a water-mediated hydrogen bond with the O1 atom of GlcNAc at subsite -1, and a mechanism of Grotthuss proton transfer was proposed <cite>chihaya2017</cite>. However, subsequent crystallographic reports on three GH136 lacto-''N''-biosidases ("Er"Lnb136, BsaX, and TnX) revealed a direct hydrogen bond between the acid/base catalyst and the O1 atom. This observation suggests that a direct proton transfer mechanism is prevalent within this family <cite>Michael2020 Yamada2022</cite>.

== Catalytic Residues ==
For LnbX, the nucleophile and the catalytic acid/base are Asp418 and Asp411, respectively.

== Three-dimensional structures ==
[[file:LnbXc.png|thumb|300px|right|'''Figure 1: '''Overall structure of LnbXc with LNB (cyan) and two Ca2+ ions (orange).]]
[[file:ErGH136.png|thumb|300px|right|'''Figure 2: '''Overall structure of ''Er''Lnb136 with LNB (yellow), consisting of an N-terminal domain designated as ''Er''Lnb136I (cyan-blue) and a C-terminal β-helix domain (green) -''Er''Lnb136II.]]

The X-ray crystal structure of the catalytic domain, LnbXc(31-625) revealed a right-handed β helix fold that is usually shared by polysaccharide-active enzymes. Three forms, ligand free at 2.36 Å resolution (PDB ID 5GQC), LNB complex at 1.82 Å (PDB ID 5GQF), and GNB complex at 2.70 Å (PDB ID 5GQG) were determined <cite>chihaya2017</cite>.
The X-ray crystal structure of '' Er''GH136 in complex with LNB (PDB ID 6KQT) revealed the N-terminal domain (''Er''Lnb136I, from AA 7-224) consists of 8 α-helices (α1-α8) and Y145 of the α6-α7 loop positioned near the active site <cite>Michael2020</cite>. The LNB-complexed structures of the catalytic domain of BsaX from ''Bifidobacterium saguini'' and TnX from ''Tyzzerella nexilis'' were also reported <cite>Yamada2022</cite>.

== Family Firsts ==
;First stereochemistry determination: LnbX from ''Bifidobacterium longum'' <cite>Sakurama2013</cite>.
;First catalytic nucleophile identification: LnbX from ''Bifidobacterium longum'' <cite>chihaya2017</cite>.
;First general acid/base residue identification: LnbX from ''Bifidobacterium longum'' <cite>chihaya2017</cite>.
;First 3-D structure: LnbX from ''Bifidobacterium longum'' <cite>chihaya2017</cite>.

== References ==
<biblio>
#Sakurama2013 pmid=23843461
#Gotoh2015 pmid=25839135
#chihaya2017 pmid=28392148
#Michael2020 pmid=32620774
#Yamada2020 pmid=35092420
</biblio>

[[Category:Glycoside Hydrolase Families|GH136]]

User:Shinya Fushinobu

2023-06-16T03:23:20Z

Shinya Fushinobu:

[[Image:Fushinobu3.jpg|200px|right]]

I am a Professor at [http://enzyme13.bt.a.u-tokyo.ac.jp/index-e.html Laboratory of Enzymology] in Department of Biotechnology, [http://www.a.u-tokyo.ac.jp/english/index.html Graduate School of Agricultural and Life Sciences], [http://www.u-tokyo.ac.jp/index_e.html The University of Tokyo] located in Tokyo, Japan. Raised in [http://www.city.kure.hiroshima.jp/site/userguide/foreign.html Kure], Hiroshima, Japan. I obtained Ph.D degree in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern structure and function of enzymes, mainly those of Carbohydrate-Active enZymes. My home page is [http://enzyme13.bt.a.u-tokyo.ac.jp/fushi/index-e.html here]. I contributed to three-dimensional structure determination of

*[[GH1]] ''Phanerochaete chrysosporium'' β-glucosidase 1B (BGL1B) <cite>Nijikken2007</cite>
*[[GH1]] Metagenomic β-Glucosidase (Td2F2) <cite>Matsuzawa2016</cite>
*[[GH1]] ''Bacillus'' sp. pyruvylated galactosidase (PvGal-ase) <cite>Higuchi2018</cite>
*[[GH3]] ''Kluyveromyces marxianus'' β-glucosidase (''Km''BglI) <cite>Yoshida2010</cite>
*[[GH3]] ''Aspergillus aculeatus'' β-glucosidase (''Aa''BGL1) <cite>Suzuki2013</cite>
*[[GH5]] ''Talaromyces trachyspermus'' β-mannanase (TtMan5A ) <cite>Suzuki2018</cite>
*[[GH8]] ''Bacillus halodurans'' reducing-end xylose-releasing exo-oligoxylanase (Rex) <cite>Fushinobu2005</cite>
*[[GH9]] ''Photobacterium profundum'' exo-β-D-glucosaminidase (PpGlcNase) <cite>Honda2016</cite>
*[[GH10]] ''Clostridium stercorarium'' xylanase B (XynB) <cite>Nishimoto2007</cite>
*[[GH11]] ''Aspergillus kawachii'' xylanase C (XynC) <cite>Fushinobu1998</cite>
*[[GH13]] ''Arthrobacter globiformis'' cyclic α-maltosyl-(1→6)-maltose hydrolase (CMMase) <cite>Kohno2018</cite>
*[[GH18]] ''Cordyceps militaris'' endo-β-''N''-acetylglucosaminidase (Endo-CoM) <cite>Seki2019</cite>
*[[GH20]] ''Bifidobacterium bifidum'' lacto-''N''-biosidase (''Bb''LNBase) <cite>Ito2013</cite>
*[[GH20]] ''Bifidobacterium bifidum'' sulfoglycosidase (BbhII) <cite>Katoh2023</cite>
*[[GH26]] β-mannanase from a symbiotic protist of the termite ''Reticulitermes speratus'' (''Rs''Man26C) <cite>Tsukagoshi2014</cite>
*[[GH29]] ''Bifidobacterium longum'' subsp. ''infantis'' 1,3-1,4-α-L-fucosidase (''Bi''AfcB) <cite>Sakurama2012</cite>
*[[GH42]] ''Thermus thermophilus'' β-galactosidase (A4-β-Gal) '''Family First''' <cite>Hidaka2002</cite>
*[[GH42]] ''Bifidobacterium animalis'' subsp. ''lactis'' α-L-arabinopyranosidase (''Bl''Arap42B) <cite>Viborg2017</cite>
*[[GH42]] ''Bifidobacterium longum'' subsp. ''infantis'' β-galctosidase (''Bi''Bga42A) <cite>Gotoh2023</cite>
*[[GH45]] ''Phanerochaete chrysosporium'' endoglucanase (PcCel45A) <cite>Nakamura2015</cite>
*[[GH51]] ''Thermotoga maritima'' α-L-arabinofuranosidase (''Tm''-AFase) <cite>Im2012</cite>
*[[GH54]] ''Aspergillus kawachii'' α-L-arabinofuranosidase B (AkAbfB) '''Family First''' plus identification of [[CBM42]] <cite>Miyanaga2004</cite>
*[[GH55]] ''Phanerochaete chrysosporium'' β-1,3-glucanase (Lam55A) '''Family First''' <cite>Ishida2009</cite>
*[[GH57]] ''Thermococcus litoralis'' 4-α-glucanotransferase (TLGT) '''Family First''' <cite>Imamura2003</cite>
*[[GH65]] ''Caldicellulosiruptor saccharolyticus'' kojibiose phosphorylase (CsKP) <cite>Okada2013</cite>
*[[GH65]] ''Bacillus selenitireducens'' 2-''O''-α-glucosylglycerol phosphorylase (GGP) <cite>Touhara2014</cite>
*[[GH79]] ''Fusarium oxysporum'' 4-''O''-α-L-rhamnosyl-β-D-glucuronidase (FoBGlcA) <cite>Kondo2021A</cite>
*[[GH94]] ''Vibrio proteolyticus'' chitobiose phosphorylase (ChBP) '''Family First''' <cite>Hidaka2004</cite>
*[[GH94]] ''Cellvibrio gilvus'' cellobiose phosphorylase (CBP) <cite>Hidaka2006</cite>
*[[GH94]] ''Saccharophagus degradans'' cellobionic acid phosphorylase (CABP) <cite>Nam2015</cite>
*[[GH94]] ''Lachnoclostridium phytofermentans'' 1,2-β-oligoglucan phosphorylase (LpSOGP) <cite>Nakajima2017</cite>
*[[GH101]] ''Bifidobacterium longum'' endo-α-''N''-acetylgalactosaminidase (EngBF) <cite>Suzuki2009</cite>
*[[GH112]] ''Bifidobacterium longum'' galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) '''Family First''' <cite>Hidaka2009</cite>
*[[GH121]] ''Bifidobacterium longum'' β-L-arabinobiosidase (HypBA2) '''Family First''' <cite>Saito2020</cite>
*[[GH127]] ''Bifidobacterium longum'' β-L-arabinofuranosidase (HypBA1) '''Family First''' <cite>Ito2014</cite>
*[[GH129]] ''Bifidobacterium bifidum'' α-''N''-acetylgalactosaminidase (NagBb) '''Family First''' <cite>Sato2017</cite>
*[[GH130]] ''Listeria innocua'' β-1,2-mannobiose phosphorylase (Lin0857) <cite>Tsuda2015</cite>
*[[GH136]] ''Bifidobacterium longum'' lacto-''N''-biosidase (LnbX) '''Family First''' <cite>Yamada2017</cite>
*[[GH136]] ''Eubacterium ramulus'' lacto-''N''-biosidase (''Er''Lnb136) <cite>Pichler2020</cite>
*[[GH136]] ''Bifidobacterium saguini'' lacto-''N''-biosidase (BsaX) <cite>Yamada2022</cite>
*[[GH136]] ''Tyzzerella nexilis'' lacto-''N''-biosidase (TnX) <cite>Yamada2022</cite>
*[[GH144]] ''Chitinophaga pinensis'' endo-β-1,2-glucanase (Cpin_6279) '''Family First''' <cite>Abe2017</cite>
*[[GH172]] ''Bifidobacterium dentium'' difructose dianhydride I synthase/hydrolase (αFFase1) '''Family First''' <cite>Kashima2021</cite>
*[[PL20]] ''Trichoderma reesei'' endo-β-1,4-glucuronan lyase (TrGL) '''Family First''' <cite>Konno2009</cite>
*[[PL42]] ''Fusarium oxysporum'' L-rhamnose-α-1,4-D-glucuronate lyase (FoRham1) '''Family First''' <cite>Kondo2021B</cite>
*[[CBM28]] in ''Clostridium josui'' Cel5A (''Cj''CBM28) <cite>Tsukimoto2010</cite>

----

<biblio>
#Nijikken2007 pmid=17376440
#Yoshida2010 pmid=20662765
#Suzuki2013 pmid=23537284
#Fushinobu2005 pmid=15718242
#Nishimoto2007 pmid=17383976
#Fushinobu1998 pmid=9930661
#Ito2013 pmid=23479733
#Tsukagoshi2014 pmid=24570006
#Sakurama2012 pmid=22451675
#Hidaka2002 pmid=12215416
#Miyanaga2004 pmid=15292273
#Ishida2009 pmid=19193645
#Imamura2003 pmid=12618437
#Okada2013 pmid=24255995
#Hidaka2004 pmid=15274915
#Hidaka2006 pmid=16646954
#Suzuki2009 pmid=19502354
#Hidaka2009 pmid=19124470
#Konno2009 pmid=19306878
#Tsukimoto2010 pmid=20159017
#Im2012 pmid=22313787
#Ito2014 pmid=24680821
#Touhara2014 pmid=24828502
#Nam2015 pmid=26041776
#Nakamura2015 pmid=26601228
#Tsuda2015 pmid=26632508
#Honda2016 pmid=26621872
#Matsuzawa2016 pmid=27092463
#Nakajima2017 pmid=28198470
#Abe2017 pmid=28270506
#Yamada2017 pmid=28392148
#Sato2017 pmid=28546425
#Viborg2017 pmid=29061847
#Suzuki2018 Suzuki K, Michikawa M, Sato H, Yuki M, Kamino K, Ogasawara W, Fushinobu S, and Kaneko S. (2018) Purification, cloning, functional expression, structure, and characterization of a thermostable β-mannanase from ''Talaromyces trachyspermus'' B168 and its efficiency in production of mannooligosaccharides from coffee wastes. ''J. Appl. Glycosci.'' '''65''', 13-21. [https://doi.org/10.5458/jag.jag.JAG-2017_018 DOI: 10.5458/jag.jag.JAG-2017_018]
#Higuchi2018 pmid=30104607
#Kohno2018 pmid=30181215
#Seki2019 pmid=31548313
#Saito2020 pmid=32479540
#Pichler2020 pmid=32620774
#Kondo2021A pmid=33645879
#Kondo2021B pmid=34303708
#Kashima2021 pmid=34688653
#Yamada2022 pmid=35092420
#Katoh2023 pmid=36864192
#Gotoh2023 Gotoh A, Hidaka M, Sakurama H, Nishimoto M, Kitaoka M, Sakanaka M, Fushinobu S, and Katayama T. (2023) Substrate recognition mode of a glycoside hydrolase family 42 β-galactosidase from ''Bifidobacterium longum'' subspecies ''infantis'' (''Bi''Bga42A) revealed by crystallographic and mutational analyses. ''Microbiome Res. Rep.'''''2''', 20. [https://doi.org/10.20517/mrr.2023.14 DOI: 10.20517/mrr.2023.14]
</biblio>

[[Category:Contributors|Fushinobu, Shinya]]

User:Shinya Fushinobu

2023-06-16T03:21:25Z

Shinya Fushinobu:

[[Image:Fushinobu3.jpg|200px|right]]

I am a Professor at [http://enzyme13.bt.a.u-tokyo.ac.jp/index-e.html Laboratory of Enzymology] in Department of Biotechnology, [http://www.a.u-tokyo.ac.jp/english/index.htmlGraduate School of Agricultural and Life Sciences], [http://www.u-tokyo.ac.jp/index_e.html The University of Tokyo] located in Tokyo, Japan. Raised in [http://www.city.kure.hiroshima.jp/site/userguide/foreign.html Kure], Hiroshima, Japan. I obtained Ph.D degree in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern structure and function of enzymes, mainly those of Carbohydrate-Active enZymes. My home page is [http://enzyme13.bt.a.u-tokyo.ac.jp/fushi/index-e.html here]. I contributed to three-dimensional structure determination of

*[[GH1]] ''Phanerochaete chrysosporium'' β-glucosidase 1B (BGL1B) <cite>Nijikken2007</cite>
*[[GH1]] Metagenomic β-Glucosidase (Td2F2) <cite>Matsuzawa2016</cite>
*[[GH1]] ''Bacillus'' sp. pyruvylated galactosidase (PvGal-ase) <cite>Higuchi2018</cite>
*[[GH3]] ''Kluyveromyces marxianus'' β-glucosidase (''Km''BglI) <cite>Yoshida2010</cite>
*[[GH3]] ''Aspergillus aculeatus'' β-glucosidase (''Aa''BGL1) <cite>Suzuki2013</cite>
*[[GH5]] ''Talaromyces trachyspermus'' β-mannanase (TtMan5A ) <cite>Suzuki2018</cite>
*[[GH8]] ''Bacillus halodurans'' reducing-end xylose-releasing exo-oligoxylanase (Rex) <cite>Fushinobu2005</cite>
*[[GH9]] ''Photobacterium profundum'' exo-β-D-glucosaminidase (PpGlcNase) <cite>Honda2016</cite>
*[[GH10]] ''Clostridium stercorarium'' xylanase B (XynB) <cite>Nishimoto2007</cite>
*[[GH11]] ''Aspergillus kawachii'' xylanase C (XynC) <cite>Fushinobu1998</cite>
*[[GH13]] ''Arthrobacter globiformis'' cyclic α-maltosyl-(1→6)-maltose hydrolase (CMMase) <cite>Kohno2018</cite>
*[[GH18]] ''Cordyceps militaris'' endo-β-''N''-acetylglucosaminidase (Endo-CoM) <cite>Seki2019</cite>
*[[GH20]] ''Bifidobacterium bifidum'' lacto-''N''-biosidase (''Bb''LNBase) <cite>Ito2013</cite>
*[[GH20]] ''Bifidobacterium bifidum'' sulfoglycosidase (BbhII) <cite>Katoh2023</cite>
*[[GH26]] β-mannanase from a symbiotic protist of the termite ''Reticulitermes speratus'' (''Rs''Man26C) <cite>Tsukagoshi2014</cite>
*[[GH29]] ''Bifidobacterium longum'' subsp. ''infantis'' 1,3-1,4-α-L-fucosidase (''Bi''AfcB) <cite>Sakurama2012</cite>
*[[GH42]] ''Thermus thermophilus'' β-galactosidase (A4-β-Gal) '''Family First''' <cite>Hidaka2002</cite>
*[[GH42]] ''Bifidobacterium animalis'' subsp. ''lactis'' α-L-arabinopyranosidase (''Bl''Arap42B) <cite>Viborg2017</cite>
*[[GH42]] ''Bifidobacterium longum'' subsp. ''infantis'' β-galctosidase (''Bi''Bga42A) <cite>Gotoh2023</cite>
*[[GH45]] ''Phanerochaete chrysosporium'' endoglucanase (PcCel45A) <cite>Nakamura2015</cite>
*[[GH51]] ''Thermotoga maritima'' α-L-arabinofuranosidase (''Tm''-AFase) <cite>Im2012</cite>
*[[GH54]] ''Aspergillus kawachii'' α-L-arabinofuranosidase B (AkAbfB) '''Family First''' plus identification of [[CBM42]] <cite>Miyanaga2004</cite>
*[[GH55]] ''Phanerochaete chrysosporium'' β-1,3-glucanase (Lam55A) '''Family First''' <cite>Ishida2009</cite>
*[[GH57]] ''Thermococcus litoralis'' 4-α-glucanotransferase (TLGT) '''Family First''' <cite>Imamura2003</cite>
*[[GH65]] ''Caldicellulosiruptor saccharolyticus'' kojibiose phosphorylase (CsKP) <cite>Okada2013</cite>
*[[GH65]] ''Bacillus selenitireducens'' 2-''O''-α-glucosylglycerol phosphorylase (GGP) <cite>Touhara2014</cite>
*[[GH79]] ''Fusarium oxysporum'' 4-''O''-α-L-rhamnosyl-β-D-glucuronidase (FoBGlcA) <cite>Kondo2021A</cite>
*[[GH94]] ''Vibrio proteolyticus'' chitobiose phosphorylase (ChBP) '''Family First''' <cite>Hidaka2004</cite>
*[[GH94]] ''Cellvibrio gilvus'' cellobiose phosphorylase (CBP) <cite>Hidaka2006</cite>
*[[GH94]] ''Saccharophagus degradans'' cellobionic acid phosphorylase (CABP) <cite>Nam2015</cite>
*[[GH94]] ''Lachnoclostridium phytofermentans'' 1,2-β-oligoglucan phosphorylase (LpSOGP) <cite>Nakajima2017</cite>
*[[GH101]] ''Bifidobacterium longum'' endo-α-''N''-acetylgalactosaminidase (EngBF) <cite>Suzuki2009</cite>
*[[GH112]] ''Bifidobacterium longum'' galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) '''Family First''' <cite>Hidaka2009</cite>
*[[GH121]] ''Bifidobacterium longum'' β-L-arabinobiosidase (HypBA2) '''Family First''' <cite>Saito2020</cite>
*[[GH127]] ''Bifidobacterium longum'' β-L-arabinofuranosidase (HypBA1) '''Family First''' <cite>Ito2014</cite>
*[[GH129]] ''Bifidobacterium bifidum'' α-''N''-acetylgalactosaminidase (NagBb) '''Family First''' <cite>Sato2017</cite>
*[[GH130]] ''Listeria innocua'' β-1,2-mannobiose phosphorylase (Lin0857) <cite>Tsuda2015</cite>
*[[GH136]] ''Bifidobacterium longum'' lacto-''N''-biosidase (LnbX) '''Family First''' <cite>Yamada2017</cite>
*[[GH136]] ''Eubacterium ramulus'' lacto-''N''-biosidase (''Er''Lnb136) <cite>Pichler2020</cite>
*[[GH136]] ''Bifidobacterium saguini'' lacto-''N''-biosidase (BsaX) <cite>Yamada2022</cite>
*[[GH136]] ''Tyzzerella nexilis'' lacto-''N''-biosidase (TnX) <cite>Yamada2022</cite>
*[[GH144]] ''Chitinophaga pinensis'' endo-β-1,2-glucanase (Cpin_6279) '''Family First''' <cite>Abe2017</cite>
*[[GH172]] ''Bifidobacterium dentium'' difructose dianhydride I synthase/hydrolase (αFFase1) '''Family First''' <cite>Kashima2021</cite>
*[[PL20]] ''Trichoderma reesei'' endo-β-1,4-glucuronan lyase (TrGL) '''Family First''' <cite>Konno2009</cite>
*[[PL42]] ''Fusarium oxysporum'' L-rhamnose-α-1,4-D-glucuronate lyase (FoRham1) '''Family First''' <cite>Kondo2021B</cite>
*[[CBM28]] in ''Clostridium josui'' Cel5A (''Cj''CBM28) <cite>Tsukimoto2010</cite>

----

<biblio>
#Nijikken2007 pmid=17376440
#Yoshida2010 pmid=20662765
#Suzuki2013 pmid=23537284
#Fushinobu2005 pmid=15718242
#Nishimoto2007 pmid=17383976
#Fushinobu1998 pmid=9930661
#Ito2013 pmid=23479733
#Tsukagoshi2014 pmid=24570006
#Sakurama2012 pmid=22451675
#Hidaka2002 pmid=12215416
#Miyanaga2004 pmid=15292273
#Ishida2009 pmid=19193645
#Imamura2003 pmid=12618437
#Okada2013 pmid=24255995
#Hidaka2004 pmid=15274915
#Hidaka2006 pmid=16646954
#Suzuki2009 pmid=19502354
#Hidaka2009 pmid=19124470
#Konno2009 pmid=19306878
#Tsukimoto2010 pmid=20159017
#Im2012 pmid=22313787
#Ito2014 pmid=24680821
#Touhara2014 pmid=24828502
#Nam2015 pmid=26041776
#Nakamura2015 pmid=26601228
#Tsuda2015 pmid=26632508
#Honda2016 pmid=26621872
#Matsuzawa2016 pmid=27092463
#Nakajima2017 pmid=28198470
#Abe2017 pmid=28270506
#Yamada2017 pmid=28392148
#Sato2017 pmid=28546425
#Viborg2017 pmid=29061847
#Suzuki2018 Suzuki K, Michikawa M, Sato H, Yuki M, Kamino K, Ogasawara W, Fushinobu S, and Kaneko S. (2018) Purification, cloning, functional expression, structure, and characterization of a thermostable β-mannanase from ''Talaromyces trachyspermus'' B168 and its efficiency in production of mannooligosaccharides from coffee wastes. ''J. Appl. Glycosci.'' '''65''', 13-21. [https://doi.org/10.5458/jag.jag.JAG-2017_018 DOI: 10.5458/jag.jag.JAG-2017_018]
#Higuchi2018 pmid=30104607
#Kohno2018 pmid=30181215
#Seki2019 pmid=31548313
#Saito2020 pmid=32479540
#Pichler2020 pmid=32620774
#Kondo2021A pmid=33645879
#Kondo2021B pmid=34303708
#Kashima2021 pmid=34688653
#Yamada2022 pmid=35092420
#Katoh2023 pmid=36864192
#Gotoh2023 Gotoh A, Hidaka M, Sakurama H, Nishimoto M, Kitaoka M, Sakanaka M, Fushinobu S, and Katayama T. (2023) Substrate recognition mode of a glycoside hydrolase family 42 β-galactosidase from ''Bifidobacterium longum'' subspecies ''infantis'' (''Bi''Bga42A) revealed by crystallographic and mutational analyses. ''Microbiome Res. Rep.'''''2''', 20. [https://doi.org/10.20517/mrr.2023.14 DOI: 10.20517/mrr.2023.14]
</biblio>

[[Category:Contributors|Fushinobu, Shinya]]

Glycoside Hydrolase Family 136

2023-06-16T02:45:48Z

Shinya Fushinobu: Mechanism and family firsts

User:Chihaya Yamada

2020-08-11T03:15:51Z

Shinya Fushinobu:

[[Image:chihaya.JPG|200px|right]]

Chihaya Yamada is an assistant professor at the Laboratory of Enzymology in the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo located in Tokyo, Japan. I obtained Ph.D degree in Agriculture at The University of Tokyo in 2013. I contributed to structural analysis of lacto-''N''-biosidase (LnbX) from ''Bifidobacterium longum'' subsp. ''longum'' belonging to [[GH136]] with Prof. Shinya Fushinobu and Prof. Takane Katayama <cite>chihaya2017</cite>. My reseach interests are new enzymes from human gut microbiota.

----

<biblio>
#chihaya2017 pmid=28392148
#Michael2020 pmid=32620774

</biblio>


[[Category:Contributors|Yamada,Chihaya]]

User:Shinya Fushinobu

2020-08-06T09:46:12Z

Shinya Fushinobu:

[[Image:Fushinobu3.jpg|200px|right]]

I am a Professor at [http://enzyme13.bt.a.u-tokyo.ac.jp/index-e.html Laboratory of Enzymology] in Department of Biotechnology, [http://www.a.u-tokyo.ac.jp/english/index.html Graduate School of Agricultural and Life Sciences], [http://www.u-tokyo.ac.jp/index_e.html The University of Tokyo] located in Tokyo, Japan. Raised in [http://www.city.kure.hiroshima.jp/site/userguide/foreign.html Kure], Hiroshima, Japan. I obtained Ph.D degree in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern structure and function of enzymes, mainly those of Carbohydrate-Active enZymes. My home page is [http://enzyme13.bt.a.u-tokyo.ac.jp/fushi/index-e.html here]. I contributed to three-dimensional structure determination of

*[[GH1]] ''Phanerochaete chrysosporium'' β-glucosidase 1B (BGL1B) <cite>Nijikken2007</cite>
*[[GH1]] Metagenomic β-Glucosidase (Td2F2) <cite>Matsuzawa2016</cite>
*[[GH1]] ''Bacillus'' sp. pyruvylated galactosidase (PvGal-ase) <cite>Higuchi2018</cite>
*[[GH3]] ''Kluyveromyces marxianus'' β-glucosidase (''Km''BglI) <cite>Yoshida2010</cite>
*[[GH3]] ''Aspergillus aculeatus'' β-glucosidase (''Aa''BGL1) <cite>Suzuki2013</cite>
*[[GH5]] ''Talaromyces trachyspermus'' β-mannanase (TtMan5A ) <cite>Suzuki2018</cite>
*[[GH8]] ''Bacillus halodurans'' reducing-end xylose-releasing exo-oligoxylanase (Rex) <cite>Fushinobu2005</cite>
*[[GH9]] ''Photobacterium profundum'' exo-β-D-glucosaminidase (PpGlcNase) <cite>Honda2016</cite>
*[[GH10]] ''Clostridium stercorarium'' xylanase B (XynB) <cite>Nishimoto2007</cite>
*[[GH11]] ''Aspergillus kawachii'' xylanase C (XynC) <cite>Fushinobu1998</cite>
*[[GH13]] ''Arthrobacter globiformis'' cyclic α-maltosyl-(1→6)-maltose hydrolase (CMMase) <cite>Kohno2018</cite>
*[[GH18]] ''Cordyceps militaris'' endo-β-''N''-acetylglucosaminidase (Endo-CoM) <cite>Seki2019</cite>
*[[GH20]] ''Bifidobacterium bifidum'' lacto-''N''-biosidase (''Bb''LNBase) <cite>Ito2013</cite>
*[[GH26]] β-mannanase from a symbiotic protist of the termite ''Reticulitermes speratus'' (''Rs''Man26C) <cite>Tsukagoshi2014</cite>
*[[GH29]] ''Bifidobacterium longum'' subsp. ''infantis'' 1,3-1,4-α-L-fucosidase (''Bi''AfcB) <cite>Sakurama2012</cite>
*[[GH42]] ''Thermus thermophilus'' β-galactosidase (A4-β-Gal) '''Family First''' <cite>Hidaka2002</cite>
*[[GH42]] ''Bifidobacterium animalis'' subsp. ''lactis'' α-L-arabinopyranosidase (''Bl''Arap42B) <cite>Viborg2017</cite>
*[[GH45]] ''Phanerochaete chrysosporium'' endoglucanase (PcCel45A) <cite>Nakamura2015</cite>
*[[GH51]] ''Thermotoga maritima'' α-L-arabinofuranosidase (''Tm''-AFase) <cite>Im2012</cite>
*[[GH54]] ''Aspergillus kawachii'' α-L-arabinofuranosidase B (AkAbfB) '''Family First''' plus identification of [[CBM42]] <cite>Miyanaga2004</cite>
*[[GH55]] ''Phanerochaete chrysosporium'' β-1,3-glucanase (Lam55A) '''Family First''' <cite>Ishida2009</cite>
*[[GH57]] ''Thermococcus litoralis'' 4-α-glucanotransferase (TLGT) '''Family First''' <cite>Imamura2003</cite>
*[[GH65]] ''Caldicellulosiruptor saccharolyticus'' kojibiose phosphorylase (CsKP) <cite>Okada2013</cite>
*[[GH65]] ''Bacillus selenitireducens'' 2-''O''-α-glucosylglycerol phosphorylase (GGP) <cite>Touhara2014</cite>
*[[GH94]] ''Vibrio proteolyticus'' chitobiose phosphorylase (ChBP) '''Family First''' <cite>Hidaka2004</cite>
*[[GH94]] ''Cellvibrio gilvus'' cellobiose phosphorylase (CBP) <cite>Hidaka2006</cite>
*[[GH94]] ''Saccharophagus degradans'' cellobionic acid phosphorylase (CABP) <cite>Nam2015</cite>
*[[GH94]] ''Lachnoclostridium phytofermentans'' 1,2-β-oligoglucan phosphorylase (LpSOGP) <cite>Nakajima2017</cite>
*[[GH101]] ''Bifidobacterium longum'' endo-α-''N''-acetylgalactosaminidase (EngBF) <cite>Suzuki2009</cite>
*[[GH112]] ''Bifidobacterium longum'' galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) '''Family First''' <cite>Hidaka2009</cite>
*[[GH121]] ''Bifidobacterium longum'' β-L-arabinobiosidase (HypBA2) '''Family First''' <cite>Saito2020</cite>
*[[GH127]] ''Bifidobacterium longum'' β-L-arabinofuranosidase (HypBA1) '''Family First''' <cite>Ito2014</cite>
*[[GH129]] ''Bifidobacterium bifidum'' α-''N''-acetylgalactosaminidase (NagBb) '''Family First''' <cite>Sato2017</cite>
*[[GH130]] ''Listeria innocua'' β-1,2-mannobiose phosphorylase (Lin0857) <cite>Tsuda2015</cite>
*[[GH136]] ''Bifidobacterium longum'' lacto-''N''-biosidase (LnbX) '''Family First''' <cite>Yamada2017</cite>
*[[GH136]] ''Eubacterium ramulus'' lacto-''N''-biosidase (''Er''Lnb136) <cite>Pichler2020</cite>
*[[GH144]] ''Chitinophaga pinensis'' endo-β-1,2-glucanase (Cpin_6279) '''Family First''' <cite>Abe2017</cite>
*[[PL20]] ''Trichoderma reesei'' endo-β-1,4-glucuronan lyase (TrGL) '''Family First''' <cite>Konno2009</cite>
*[[CBM28]] in ''Clostridium josui'' Cel5A (''Cj''CBM28) <cite>Tsukimoto2010</cite>

----

<biblio>
#Nijikken2007 pmid=17376440
#Yoshida2010 pmid=20662765
#Suzuki2013 pmid=23537284
#Fushinobu2005 pmid=15718242
#Nishimoto2007 pmid=17383976
#Fushinobu1998 pmid=9930661
#Ito2013 pmid=23479733
#Tsukagoshi2014 pmid=24570006
#Sakurama2012 pmid=22451675
#Hidaka2002 pmid=12215416
#Miyanaga2004 pmid=15292273
#Ishida2009 pmid=19193645
#Imamura2003 pmid=12618437
#Okada2013 pmid=24255995
#Hidaka2004 pmid=15274915
#Hidaka2006 pmid=16646954
#Suzuki2009 pmid=19502354
#Hidaka2009 pmid=19124470
#Konno2009 pmid=19306878
#Tsukimoto2010 pmid=20159017
#Im2012 pmid=22313787
#Ito2014 pmid=24680821
#Touhara2014 pmid=24828502
#Nam2015 pmid=26041776
#Nakamura2015 pmid=26601228
#Tsuda2015 pmid=26632508
#Honda2016 pmid=26621872
#Matsuzawa2016 pmid=27092463
#Nakajima2017 pmid=28198470
#Abe2017 pmid=28270506
#Yamada2017 pmid=28392148
#Sato2017 pmid=28546425
#Viborg2017 pmid=29061847
#Suzuki2018 Suzuki K, Michikawa M, Sato H, Yuki M, Kamino K, Ogasawara W, Fushinobu S, and Kaneko S. (2018) Purification, cloning, functional expression, structure, and characterization of a thermostable β-mannanase from ''Talaromyces trachyspermus'' B168 and its efficiency in production of mannooligosaccharides from coffee wastes. ''J. Appl. Glycosci.'' '''65''', 13-21. [https://doi.org/10.5458/jag.jag.JAG-2017_018 DOI: 10.5458/jag.jag.JAG-2017_018]
#Higuchi2018 pmid=30104607
#Kohno2018 pmid=30181215
#Seki2019 pmid=31548313
#Saito2020 pmid=32479540
#Pichler2020 pmid=32620774
</biblio>

[[Category:Contributors|Fushinobu, Shinya]]

File:GH121-HypBA2.png

2020-08-06T08:58:41Z

Shinya Fushinobu: Shinya Fushinobu uploaded a new version of File:GH121-HypBA2.png

Crystal structure of GH121 HypBA2 from ''Bifidobacterium longum'' JCM 1217.
PMID: 32479540

File:GH121-HypBA2.png

2020-08-06T08:56:55Z

Shinya Fushinobu: Crystal structure of GH121 HypBA2 from ''Bifidobacterium longum'' JCM 1217. PMID: 32479540

Crystal structure of GH121 HypBA2 from ''Bifidobacterium longum'' JCM 1217.
PMID: 32479540

Glycoside Hydrolase Family 121

2020-08-06T08:55:19Z

Shinya Fushinobu: Crystal structure paper updated.

{{CuratorApproved}}
* [[Author]]: ^^^Kiyotaka Fujita^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH121'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH121.html
|}
</div>


== Substrate specificities ==
This family of [[glycoside hydrolases]] contains β-L-arabinobiosidases, as demonstrated for HypBA2 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2011A</cite>. HypBA2 liberates the disaccharide Ara''f''β1-2Ara''f'' (β-Ara2, a substrate of the [[GH127]] β-L-arabinofuranosidase from ''B. longum'' JCM 1217 <cite>Fujita2011B</cite>) from unmodified Ara''f''β1-2Ara''f''β1-2Ara''f''β-hydroxyproline (Ara3-Hyp), but not Ara''f''α1-3Ara''f''β1-2Ara''f''β1-2Ara''f''β-Hyp (Ara4-Hyp) or Ara''f''β1-2Ara''f''β-Hyp (Ara2-Hyp). HypBA2 directly liberates β-Ara2 from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin. The family members are only found from prokaryote genomes, such as bacteria and actinomycetes.

== Kinetics and Mechanism ==
HypBA2 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol; the resulting Ara''f''β1-2Ara''f''β-Me was identified by 1H-NMR and 13C-NMR analysis.

== Catalytic Residues ==
The catalytic residues are not known but three conserved residues (Glu373, Asp515, and Glu713 in ''B. longum'' HypBA2) are the candidates based on mutagenesis and structural comparison <cite>Saito2020</cite>.

== Three-dimensional structures ==
[[Image:GH121-HypBA2.png|'''Figure 1:''' β-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum''. The catalytic (α/α)6 barrel domain is in green.|frame|right]]
The first solved 3-D structure was β-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum'' (PDB [{{PDBlink}}6m5a 6M5A]) <cite>Saito2020</cite>. The catalytic domain adops an (α/α)6 barrel fold similar to [[GH142]], [[GH63]], [[GH78]], [[GH94]], and [[GH37]] ('''Figure 1''').

== Family Firsts ==
;First stereochemistry determination: Shown to be [[retaining]] for HypBA2 enzyme by measurement of glycosyl transfer reactions to methanol and the 1H-NMR and 13C-NMR spectra <cite>Fujita2011A</cite>.
;First catalytic nucleophile identification: No experimental proof.
;First general acid/base residue identification: No experimental proof.
;First 3-D structure: β-L-arabinobiosidase HypBA2 from ''Bifidobacterium longum'' <cite>Saito2020</cite>.

== References ==
<biblio>
#Fujita2011A pmid=21149454
#Fujita2011B pmid=21914802
#Saito2020 pmid=32479540
</biblio>

[[Category:Glycoside Hydrolase Families|GH121]]

Carbohydrate-binding modules

2020-07-08T04:06:10Z

Shinya Fushinobu: fixing typos

{{CuratorApproved}}
* [[Author]]: ^^^Alicia Lammerts van Bueren^^^ and ^^^Elizabeth Ficko-Blean^^^
* [[Responsible Curator]]: ^^^Al Boraston^^^ and ^^^Spencer Williams^^^
----

== Overview ==
[[Image:MvGH33modularity3.jpg||thumb|right|300px|'''Figure 1. An example of modularity in a CBM-containing glycoside hydrolase.''' Sialidase from ''Micromonospora viridifaciens'' contains an N-terminal [[CBM32]] (red) X20 linker (yellow) and a C-terminal catalytic [[GH33]] module (green) <cite>Gaskell1995</cite>. Graphical representation of modularity in amino acid sequence (top) and 3D crystal structure (bottom) PDB ID [{{PDBlink}}1eut 1eut].]]
Carbohydrate-binding modules (CBMs) <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010 Gilbert2013 Armenta2017</cite> are a class of sugar-binding proteins that comprise amino acid sequences within a larger encoded protein sequence that fold into a structurally discrete module, typically forming part of a larger multi-modular enzyme <cite>Ficko-Blean2012</cite> (Figure 1).
The conventional role of a CBM is to bind to carbohydrate ligand and direct the catalytic machinery onto its substrate, thus enhancing the catalytic efficiency of the multimodular carbohydrate-active enzyme; however, there are several key exceptions of divergent evolution in the functions of CBMs <cite>Taylor2014</cite> which are [[Carbohydrate-binding_modules#Blurred Lines: CBMs, Lectins and Outliers|discussed below]]. The individual CBMs are themselves devoid of any catalytic activity and are most commonly associated with [[Glycoside Hydrolases]] but have also been identified in [[:Category:Polysaccharide_Lyase_Families|Polysaccharide Lyases]], [[Auxiliary_Activity_Families|polysaccharide oxidases]], [[Glycosyltransferases]], plant cell wall-binding expansins <cite>Georgelis2011</cite> and in some lectins <cite>Taylor2014</cite>.

CBMs themselves do not undergo any conformational changes when binding ligand. Rather, the topography of the carbohydrate-binding site is preformed to be complementary to the shape of the target ligand (see [[#Types|Types]]). This is achieved by the presence of amino acid side chains present on the CBM binding surface or within the CBM binding cleft or pocket. Multimodular enzymes that include CBMs may as a whole be quite flexible and undergo significant conformational changes when binding substrate. Flexible Ser-Thr-Pro sequences often link adjacent modules and can allow for shifts in the orientation and direction of the catalytic module with respect to the CBM on the target substrate. In other enzymes the linking regions may be quite rigid, such as the 5-helical bundle linker module linking a [[CBM32]] to a [[GH84]] module <cite>Ficko2009</cite>.

==History of CBMs==
CBMs were initially characterized as cellulose binding domains (CBDs) in cellobiohydrolases CBHI and CBHII from ''Trichoderma reesei'' <cite>VanTilbeurgh1986 Tomme1988</cite> and cellulases CenA and CexA from ''Cellulomonas fimi'' <cite>Gilkes1988</cite>. Limited proteolysis experiments on these enzymes yielded truncated enzyme products that showed a reduced or complete loss in their ability to hydrolyze cellulose substrates. The reduction in enzymatic activity was attributed to the loss of ~100 amino acid C-terminal domains which prevented the adsorbption of the enzymes onto cellulose substrate. Thus it was proposed that these independent "domains" are critical for targeting the enzymes onto its substrate and enhancing their hydrolytic activity. It rapidly became evident that CBDs were not only appended to cellulases but were also found in a range of other plant cell wall degrading enzymes <cite>Kellett1990 Ferriera1990 Ferriera1993</cite>.

Initially, CBDs were categorized into 13 Types based on amino acid sequence similarities <cite>Tomme1995</cite>. This classification system became complicated when similar functional domains from non-cellulolytic carbohydrate-active enzymes were discovered that did not bind cellulose but met all of the [[#Criteria for Defining a new CBM family|criteria]] of a CBD (for example see <cite>Svensson1989</cite>). The term carbohydrate-binding module was proposed to solve this problem to be inclusive of all ancillary modules with non-catalytic carbohydrate-binding function (for a review see <cite>Boraston2004</cite>). Since this time, CBMs have been found appended to enzymes that interact with almost all characterized carbohydrate materials found on Earth (Table 1).

<div style="width:550px;" align="left">
{| {{Prettytable}} class="mw-collapsible mw-collapsed"
|-
| bgcolor="#F5F5F5" colspan="2" align="center"|'''Table 1: List of Carbohydrates and Interacting CBM Familiesa'''
|-
|'''Cellulose'''
|[[CBM1]], [[CBM2]], [[CBM3]], [[CBM4]], [[CBM6]], [[CBM8]], [[CBM9]], [[CBM10]], [[CBM16]], [[CBM17]], [[CBM28]], [[CBM30]], [[CBM37]], [[CBM44]], [[CBM46]], [[CBM49]], [[CBM59]], [[CBM63]], [[CBM64]]
|-
|'''Xylan'''
|[[CBM2]], [[CBM4]], [[CBM6]], [[CBM9]], [[CBM13]], [[CBM15]], [[CBM22]], [[CBM31]], [[CBM35]], [[CBM36]], [[CBM37]], [[CBM44]], [[CBM54]], [[CBM59]], [[CBM60]]
|-
|'''Plant Cell Wall - Other'''
(eg: beta-glucans, pectins, mannans, gluco- and galacturonans)'''
|[[CBM4]], [[CBM6]], [[CBM11]], [[CBM13]], [[CBM16]], [[CBM22]], [[CBM23]], [[CBM27]], [[CBM28]], [[CBM29]], [[CBM32]], [[CBM35]], [[CBM39]], [[CBM42]], [[CBM43]], [[CBM52]], [[CBM56]], [[CBM59]], [[CBM61]], [[CBM62]], [[CBM65]], [[CBM67]]
|-
|'''Chitin'''
|[[CBM1]], [[CBM2]], [[CBM3]], [[CBM5]], [[CBM12]], [[CBM14]], [[CBM18]], [[CBM19]], [[CBM37]], [[CBM50]], [[CBM54]], [[CBM55]]
|-
|'''Alpha-glucans'''
(starch/glycogen, mutan)
|[[CBM20]], [[CBM21]], [[CBM24]], [[CBM25]], [[CBM26]], [[CBM34]], [[CBM41]], [[CBM45]], [[CBM48]], [[CBM53]], [[CBM58]]
|-
|'''Mammalian Glycans'''
|[[CBM32]], [[CBM40]], [[CBM47]], [[CBM51]], [[CBM57]]b
|-
|'''Algal (seaweed) Saccharides'''
(e.g. <s>porphyran</s>, agarose, carrageenan, <s>alginate</s>, laminarin)
|[[CBM6]], [[CBM16]]
|-
|'''Other'''
|Bacterial cell wall sugars: [[CBM35]], [[CBM39]], [[CBM50]] Fructans: [[CBM38]], [[CBM66]] Yeast cell wall glucans: [[CBM54]] 
|-
|-
| colspan="2" |aBased on the [http://www.cazy.org/Carbohydrate-Binding-Modules.html Carbohydrate Active enZyme database]. [[CBM7]] is a deleted entry and [[CBM33]] is now reclassified as Auxiliary Activities family [[AA10]]. bonly human lectin malectin has been characterized, however a search based on amino acid sequence similarities found that similar modules are appended to many uncharacterized glycoside hydrolases <cite>Shallus2008</cite>.
|}
</div>

== Classification ==
=== Sequence Based Classification ===
Carbohydrate-binding modules are classified into many tens of families based on amino acid sequence similarities (a continually updated list is available in the [http://www.cazy.org/Carbohydrate-Binding-Modules.html Carbohydrate Active enZyme database]). These families often cluster modules with similar structural folds and carbohydrate-binding function. However, there are several families that exhibit diversity in the carbohydrate ligands they target (Table 1).

=== Fold ===
[[Image:CBMfold.jpg|thumb|right|500px|'''Figure 2. Classical CBM beta-sandwich fold.''' C-terminal family CBM27 from ''Thermotoga maritima'' mannanase, a Type B CBM (A)(side and front view, PDB ID [{{PDBlink}}1OF4 1OF4]) <cite>Boraston20031</cite> and C-terminal family CBM6 from ''Clostridium stercorarium'' xylanase (B) (PDB ID [{{PDBlink}}1NAE 1NAE]) <cite>Boraston20032</cite> showing binding sites on the face (A) and loop region (B) of the beta sandwich fold respectively.]]
CBMs fall into one of 7 fold families <cite>Boraston2004</cite>. The most common fold exhibited by CBMs is the beta-sandwich fold comprised of two overlapping beta-sheets each consisting of three to six antiparallel beta strands (Figure 2). The ligand binding site may be located on one face of the beta-sheet (Figure 2A) or may be positioned within the variable loop region of the beta-sheet (Figure 2B). There are examples of CBMs in the beta-sandwich fold family exhibiting dual binding sites such as [[CBM6]] <cite>Pires2004</cite> and dual starch-binding sites in [[CBM20]] <cite>Lawson1994</cite>. Other fold families include the beta-trefoil fold, cystine knot, OB fold, the hevein and hevein-like and unique folds <cite>Boraston2004</cite>. CBMs of the beta-trefoil fold family ([[CBM13]], [[CBM42]]) present multivalent sugar-binding sites, as demonstrated for their interaction with xylan and arabinoxylan respectively <cite>Fujimoto2013</cite>.

=== Types ===
[[Image:TypeAsurface.png|thumb|right|400px|'''Figure 3. CBM Types.''' (A) Schematic of different CBM Types binding with different regions of a polysaccharide substrate. (B) Type A [[CBM2]]b from ''Pyrococcus furiosis'' [[GH18]] chitinase(PDB ID [{{PDBlink}}2CRW 2CRW]) <cite>Nakamura2008</cite>. Aromatic side chains of Type A CBMs form the planar binding surface.]]
CBMs are classified into three main Types defined by the shape and degree of polymerization of their target ligand (Figure 3A). The architecture of the binding site determines what region within a saccharide macromolecule the enzyme will [[#Functional Roles of CBMs|target]]. The classification of CBM Types is as follows <cite>Gilbert2013, Armenta2017, Boraston2004</cite>:
* Type A: bind to crystalline surfaces of the polysaccharides cellulose and chitin (example families [[CBM1]], [[CBM2]], [[CBM3]], [[CBM5]], [[CBM10]]). Their binding sites are planar and rich in aromatic amino acid residues creating a flat platform to bind to the planar polycrystalline chitin/cellulose surface (Figure 3B). Type A CBMs are unique and differ significantly from Type B or C.
* Type B: bind internal glycan chains (''endo''-type). Type B are the most abundant form of CBMs reported to date. Type B binding sites appear as extended grooves or clefts comprised of binding subsites to generally accommodate longer sugar chains with four or more monosaccharide units (see Figure 2A for an example). There are some examples of CBMs, in families [[CBM6]], [[CBM13]], [[CBM20]], [[CBM36]] and [[CBM60]], that contain two subsites.
* Type C: bind termini of glycans (reducing/non-reducing ends, ''exo''-type). Type C binding sites are short pockets for recognizing short sugar ligands containing one to three monosaccharide units (example families [[CBM9]], [[CBM13]], [[CBM32]], [[CBM47]], [[CBM66]], [[CBM67]]). Families containing Type C CBMs are considered 'lectin-like' and may include lectins and CBMs with no appended catalytic modules as members.

== Properties of CBM Carbohydrate Binding Interactions ==
=== Functional Roles of CBMs ===
CBMs carry out four main functional roles:

*''Targeting Effect'': CBMs target the enzyme to distinct regions on a saccharide substrate (reducing end, non-reducing end, internal polysaccharide chains), depending on the architecture of its binding site (see [[#Types|Types]]).

*''Proximity Effect'': CBMs increase the concentration of enzyme in close proximity to its saccharide substrate. This leads to more rapid and efficient substrate degradation.

An excellent example demonstrating targeting and proximity effects of plant cell wall specific CBMs is available <cite>Herve2010</cite>.

*''Disruptive Effect'': Some CBMs have been shown to disrupt the surface of tightly packed polysaccharides, such as cellulose fibres and starch granules, causing the substrate to loosen and become more exposed to the catalytic module for more efficient degradation. Disruptive roles have been described for cellulose binding [[CBM2]]a <cite>Din1991</cite> and [[CBM44]] <cite>Gourlay2012</cite>. Dual starch-binding domains of family [[CBM20]] from ''Aspergillus niger'' glucoamylase have been shown to disrupt the surface of starch <cite>Southall1999</cite> while dual-associated [[CBM41]] modules may have a disruptive role in degrading glycogen granules <cite>vanBueren2007</cite>. [[CBM33]] was thought to have a disruptive effect on chitin, however these have now been reclassified as copper-dependent lytic polysaccharide monooxygenases <cite>Vaaje2010</cite> and are found in CAZy [[Auxiliary Activity Family 10]].

*''Adhesion'': CBMs have been shown to adhere enzymes onto the surface of bacterial cell wall components while exhibiting catalytic activity on an external neighboring carbohydrate substrate. For example, [[CBM35]] modules have been shown to interact with the surface glucuronic acid containing sugars in the cell wall of ''Amycolatopsis orientalis'' while the catalytic module is active on external chitosan likely originating from the cell wall of competing soil fungal species <cite>Montanier2009</cite>. ''Streptococcus pneumoniae'' uses a [[CBM71]] as an adhesin, to mediate adherence to host cell surfaces displaying lactose or N-acetyllactosamine <cite>king2014</cite>.

There are two examples in the literature of CBMs extending the active site sub-sites of their appended glycosidase modules. The glycogen-degrading pneumococcal virulence factor SpuA has its active site extended by one of two tandem [[CBM41]]s <cite>Lammerts2011</cite>. The glucan starch phosphatase Starch Excess4 has its active site extended by a [[CBM48]] <cite>Meekins2014</cite>.

Several lectins are classified as CBMs even though they are not on the same polypeptide chain as a carbohydrate-active enzyme. See [[Carbohydrate-binding_modules#CBMs, Lectins and Outliers|Blurred Lines: CBMs, Lectins and Outliers]] for a more complete discussion.

===Driving Forces of CBM-Carbohydrate Interactions===
There are two key features that drive CBM-carbohydrate interactions. Extensive hydrogen bonding occurs between the hydroxyl groups of carbohydrate ligands and polar amino acid residues within the binding site. Additional water-mediated hydrogen bonding networks between these groups can also be found in the binding site. By far the most important characteristic driving force mediating protein-carbohydrate interactions is the position and orientation of aromatic amino acid residues (Try, Tyr and sometimes Phe) within the binding site. These essential planar residues provide a hydrophobic platform for the planar face of sugar rings, an interaction resembling hydrophobic stacking interactions. Weak intermolecular electrostatic interactions occur between C-H and pi electrons in the planar ring systems and contribute 1.5 - 2.5 kcal/mol energy to the binding reaction <cite>Meyer2003</cite>. CBMs may also use coordinated metal ions within the binding site to directly interact with their target ligand. For example, families [[CBM36]] <cite>Jamal2004</cite> and [[CBM60]] <cite>Montanier2010</cite> exhibit calcium-dependent binding to xylooligosaccharides.

CBM-carbohydrate interactions in general are quite weak (Ka affinities in mM-1 to uM-1 range) making the interaction easily reversible. This feature allows for "recycling" of the appended enzyme to bind to a new region on the substrate once catalysis has been completed at a given site. Some CBMs that bind crystalline ligands, typified by CBM2a, bind with apparent irreversibility (they do not desorb when free CBM is diluted), displaying surface mobility and exchanging with free CBM <cite>McLean2002, Jervis1997</cite>. Multivalent effects (more than one saccharide-binding site or multiple CBMs within the polypeptide) may act to increase the overall affinity relative to a single binding site interaction.

=== CBM Promiscuity ===
Because of the diversity of carbohydrate structures and motifs found in plant and mammalian glycans, some CBMs have evolved to recognize more than one type of monosaccharide or glycosidic bond linkage within the binding pocket, a feature called CBM promiscuity. For example a family [[CBM32]] from ''Clostridium perfringens'' NagH binds N-acetyl-glucosamine in the primary subsite but can accommodate N-acetyl-galactosamine or mannose in the secondary site <cite>Ficko20092</cite>. There are several examples of ligand promiscuity within family [[CBM32]]. In plant cell wall recognizing CBMs, they are often able to accommodate both cellulose and hemicelluloses. For example, several family [[CBM6]] members interact with cellulose, xylose or laminarin <cite>Boraston20032 Lammerts2005</cite>. Family [[CBM41]] appended to a [[GH13]] pullulanase can accommodate both alpha-1,4- and alpha-1,6-linked glucose found in amylopectin (from starch/glycogen) <cite>Lammerts2007</cite>. The flexibility in carbohydrate recognition by CBMs contributes to the [[#Functional Roles of CBMs|targeting]] efficiency of carbohydrate-active enzymes in environments where there is diverse range of saccharides present (such as the plant cell wall or mammalian tissues).

=== CBMs and Multivalency ===
Multivalency is the collective strength of several interactions with a given ligand. Because CBM-carbohydrate interactions are relatively weak, some carbohydrate-active enzymes, mainly glycoside hydrolases, have developed ways to increase their interaction with substrate via a multivalent effect. Individually, some CBMs may contain multiple binding sites to form a multivalent interaction with their target ligand, although this form of multivalency is quite rare (for example [[CBM6]], [[CBM13]] and [[CBM20]]). More commonly, glycoside hydrolases may contain more than one CBM within their modular architecture, either arranged in tandem or at opposing N and C terminal ends of the protein sequence, or both. These CBMs may target the same carbohydrate ligand, different regions within the same ligand, or different ligands in a complex saccharide amalgam. A multivalent interaction enhances the overall affinity of an enzyme for its substrate. Furthermore, tandem CBMs may cooperatively target the enzyme towards specific saccharide regions based on their ligand specificity and the orientation and position of the binding sites with respect to one another.

=== Blurred Lines: CBMs, Lectins and Outliers ===
While CBMs are generally considered to be discrete entities within a polypeptide chain, there are some exceptions. The glycogen-degrading pneumococcal virulence factor SpuA has its active site extended by one of two tandem [[CBM41]]s <cite>Lammerts2011</cite> and the glucan starch phosphatase Starch Excess4 has its active site extended by a [[CBM48]] <cite>Meekins2014</cite>. Thus, the full biological contribution to carbohydrate-binding within the polypeptide is contributed by a multivalent interaction as an extension of the catalytic module's carbohydrate-binding properties. The PA14 domain is found in bacterial toxins, enzymes, adhesins and signaling molecules <cite>Rigden2004</cite>. It has been described as appended to the polypeptide sequence of some glycoside hydrolase enzymes (for example some [[GH31]]s) and the crystal structure of a [[GH31]] reveals the PA14 domain is closely associated with the catalytic module, on the side of the substrate-binding cleft, potentially facilitating the binding of longer oligosaccharides <cite>Larsbrink2011</cite>. It has also been described as a domain integrated into the core of some [[GH3]] glycoside hydrolase modules. In one example, the [[GH3]] integrated PA14 domain demonstrates carbohydrate-binding function and acts to block the active site cleft, thus conferring substrate specificity for disaccharide substrates <cite>Yoshida2010</cite>. Similarly, in a [[GH2]] mannosidase, the PA14 domain determines exo- rather than endo-activity for the catalytic module <cite>Tailford2007</cite>. Evidently, more research needs to go into the structure and function of these domains as they are found in a wide variety of polypeptide sequences and the functions of the PA14 domains may be diverse. They have not yet been classified into the CAZy classification system, though they are mentioned here as the domains have been referred to as CBMs in the literature <cite>Taylor2014</cite>.

Unrelated sugar-binding proteins have converged on similar biochemical mechanisms of saccharide recognition <cite>Taylor2014</cite>. The direct interaction of Ca2+ ions with saccharides in sugar binding sites was first described in C-type animal lectins <cite>Weis1992</cite>, named thusly because of their sugar-binding requirement for Ca2+. Other sugar-binding proteins that also require Ca2+ for binding, include yeast flocculation proteins <cite>Veelders2010</cite> and other yeast adhesins <cite>Maestre-Reyna2012, Ielasi2012</cite>, and two CBM families, [[CBM36]] and [[CBM60]] <cite>Montanier2010</cite>.

Several lectins <cite>SharonLis2004 SharonLis2007</cite> are classified as CBMs in the [http://www.cazy.org/Carbohydrate-Binding-Modules.html Carbohydrate Active enZyme database] as they share amino acid sequence similarity, exhibit similar folds and display similar carbohydrate binding properties. For example, ricin toxin B chain from ''Ricinus communis'' resides in family [[CBM13]], while wheat germ agglutinin (WGA) can be found in family [[CBM18]]. The human lectin malectin is classified as family [[CBM57]] and plays a role in N-linked glycan processing of polypeptides in the endoplasmic reticulum <cite> Shallus2008 Galli2011</cite>. CBMs may also share properties with lectins that are not (yet) incorporated in the [http://www.cazy.org/Carbohydrate-Binding-Modules.html Carbohydrate Active enZyme database]. For example, the fucose-specific ''Anquila anguila'' lectin AAA was described as similar to Type C CBMs found in family [[CBM6]] and [[CBM32]] <cite>Boraston20032</cite> and is now classified as a [[CBM47]] <cite>Boraston2006</cite>. Lectins which are classified as CBMs are incorporated into a family because they were found to share amino acid sequence identity with a known CBM appended to a carbohydrate-active enzyme. A brief historical overview of the discovery and characterization of lectins is available <cite>SharonLis2004</cite> as is a review describing the convergent and divergent mechanisms of sugar recognition across the kingdoms of life <cite>Taylor2014</cite>.

The biological reaction of agglutination is when particles that are suspended in a liquid collect into clumps, such as that occuring as a serologic response to a specific antibody. The most prominent feature that is genarally considered to separate CBMs from lectins is the involvement of lectins in agglutination of sugar-containing molecules or glycoconjugates. Lectins exploit multivalency, often forming quaternary structures as homodimers, trimers or tetramers with several binding sites which then agglutinate the target glycocongugate <cite>SharonLis2004 SharonLis2007</cite>. Few studies have been done on the agglutinating effects of CBMs or CBM tandems; however, a [[CBM26]]/[[CBM25]] pair from ''Bacillus halodurans'' is described as strongly agglutinating on soluble amylopectin (and pullulan), suggesting multivalent binding of the individual CBMs to sites on separate glucan chains <cite>Boraston2006</cite>. CBMs individually are not known to be directly involved in the formation of quaternary structures and are not known to have agglutinating properties - in common with sugar-recognition modules of all glycan-binding proteins, including lectins <cite>Taylor2014</cite>. Other examples of CBMs participating in quaternary structures but not directly implicated in quaternary structure formation are found in cellulosome complexes <cite>Freelove2001 Poole1992 Morag1995</cite> and in some secreted pathogenic bacterial enzymes complexes <cite>Adams2008 Ficko2009</cite> where complex formation is mediated through specific cohesin-dockerin module interactions.

Amino acid sequence-based classification of a CBM family may lead to the incorporation of other non-catalytic-associated CBMs within a given family. Some examples of families containing CBMs without appended catalytic modules include those with lectins (such as tachycitin ([[CBM14]]), wheat germ agglutinin ([[CBM18]]), fucolectin ([[CBM47]]), and malectin ([[CBM57]])), and those with periplasmic solute binding proteins ([[CBM32]]). Interestingly, the lectin ricin B chain ([[CBM13]]), while not on the same polypeptide chain, is covalently linked through a disulfide bond to the ricin A chain with its N-glycosidase activity <cite>Lewis1986</cite>. The ricin A chain N-glycosidase cleaves a specific adenine from the pentose ribose in ribosomal RNA <cite>Endo1987</cite>. Finally, [[CBM29]] is a family with only two members, which have no appended catalytic modules; however, the function of these CBMs is to target the catalytic cellulosome machinery to substrate <cite>Freelove2001</cite>.

==Studying CBM-ligand Interactions==
A review on approaches to studying the binding function of carbohydrate-binding modules is available <cite>Abbott2012</cite>. Typically, molecular biology techniques are used to overproduce a CBM protein in a host strain such as ''Escherichia coli'' which is then isolated and purified. Initial screening for carbohydrate binding interactions can be performed using techniques such as microarrays <cite>vanBueren2007</cite> or fluorescence microscopy <cite>vanBueren2007 McCartney2006 Herve2010</cite>. Several approaches can be taken to verify and quantify CBM-polysaccharide interaction, including affinity gel electrophoresis, UV difference and fluorescence spectroscopy, solid state depletion assay, and isothermal titration calorimetry <cite>Lammerts2004</cite>. Demonstration of carbohydrate binding function by CBMs is essential to understanding the biological role of these non-catalytic modules.

==Biotechnological applications of CBMs==
CBMs and their carbohydrate-binding properties are used for many different biological applications. Below is a non-exhaustive list of several examples:

*Features of CBMs are currently being exploited to create designer CAZymes with enhanced or modified carbohydrate recognition functions <cite>MkKee2012 Cuskin2012 McKee2012 Tang2013</cite>.

*Family [[CBM9]] can be used as an affinity tag to purify tagged proteins on a cellulose-based affinity column <cite>Kavoosi2004</cite>.

*CBMs are used as molecular probes to detect presence of specific carbohydrate motifs in plant <cite>McCartney2006 Herve2010</cite> and mammalian tissues <cite> Lammerts2007 Boraston2006</cite>.

*CBMs are used in fibre modification. Engineered CBMs have been shown to increase the strength of cellulose pulp in paper-making processes <cite>Levy2003 Yokota2009</cite>, in crosslinking polysaccharide fibres for biomaterials <cite>Levy2004</cite> and cotton fibre modification <cite>Zhang2011</cite>.

*There are several examples of CBMs being used to immobilize whole cells onto carbohydrate surfaces <cite>Francisco1993 Simsek2013 Wang2006</cite>.

*CBMs are used to enhance bioprocessing enzymes for industrial uses in pulp processing and biofuel production <cite>Reyes2013 Gourlay2012 Ravalason2009</cite>.

*Starch binding CBMs added onto transglucosylating enzyme CGTase from [[GH13]] created a fusion enzyme with more efficient transglucosylating activity with soluble starch, important for industrial biotransformation processes <cite>Han2013</cite>.

== References ==
<biblio>
#Tomme1988 pmid=3338453
#VanTilbeurgh1986 Van Tilbeurgh, H., Tomme P., Claeyssens M., Bhikhabhai R., Pettersson G.(1986) Limited proteolysis of the cellobiohydrolase I from Trichoderma reesei. FEBS Lett. 204,223–227. [http://dx.doi.org/10.1016/0014-5793(86)80816-X DOI:10.1016/0014-5793(86)80816-X]
#Gilkes1988 pmid=3134347
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Meyer2003 pmid=12645054
#Abbott2012 pmid=22608728
#vanBueren2007 pmid=17187076
#Lammerts2004 pmid=15223327
#McCartney2006 pmid=16537424
#Tomme1995 Tomme, P., Warren, R.A., Miller, R.C., Jr., Kilburn, D.G. & Gilkes, N.R. (1995) in Enzymatic Degradation of Insoluble Polysaccharides (Saddler, J.N. & Penner, M., eds.), Cellulose-binding domains: classification and properties. pp. 142-163, American Chemical Society, Washington.
#Ficko2009 pmid=19193644
#Gilbert2013 pmid=23769966
#Herve2010 pmid=20696902
#Cuskin2012 pmid=23213210
#Gaskell1995 pmid=8591030
#Vaaje2010 pmid=20929773
#Georgelis2011 pmid=21454649
#Pires2004 pmid=15010454
#Boraston20031 pmid=12791255
#Boraston20032 pmid=12634060
#Montanier2009 pmid=19218457
#Din1991 Din, N., Gilkes, N.R., Tekant, B., Miller, R.C., Jr., Warren, R.A., and Kilburn, D.G. (1991) Non-Hydrolytic Disruption of Cellulose Fibres by the Binding Domain of a Bacterial Cellulase. Nat. Biotech. 9, 1096 - 1099. [http://dx.doi.org/10.1038/nbt1191-1096 DOI:10.1038/nbt1191-1096]
#Gourlay2012 pmid=22828270
#Nakamura2008 pmid=18582475
#Galli2011 pmid=21298103
#SharonLis2004 pmid=15229195
#SharonLis2007 isbn=9781402066054
#Fujimoto2013 pmid=23832347
#Jamal2004 pmid=15242594
#Montanier2010 pmid=20659893
#Southall1999 pmid=10218582
#McKee2012 pmid=22492980
#Kavoosi2004 pmid=15177165
#Boraston2006 pmid=16987809
#Levy2003 Levy, I., Paldi, T., Siegel, D., and Shoseyov, O. (2003) ''Cellulose binding domain from Clostridium cellulovorans as a paper modification reagent.'' Nordic Pulp Paper Res. J. 18:421-428.
#Levy2004 pmid=14738848
#Yokota2009 Yokota, S., Matuso, K., Kitaoka, T., and Wariishi, H. (2009) ''Retention and paper strength characteristics of anionic polyacrylamides conjugated with carbohydrate-binding modules. "Carbohydrate-binding anionic PAM".'' BioResources 4(1):234-244 [http://ojs.cnr.ncsu.edu/index.php/BioRes/article/view/BioRes_04_1_0234_Yokota_MKW_Carohydr_Binding_aPAM/314 Article].
#Zhang2011 Zhang, Y., Chen, S., He, M., Wu, J., Chen, J., and Wang, Q. (2011) Effects of Thermobifida fusca Cutinase-carbohydrate-binding Module Fusion Proteins on Cotton Bioscouring. Biotechnology and Bioprocess Engineering. 16,645-653 [http://dx.doi.org/10.1007/s12257-011-0036-4 DOI:10.1007/s12257-011-0036-4]
#Francisco1993 pmid=7763519
#Simsek2013 pmid=23354445
#Wang2006 pmid=16391137
#Reyes2013 pmid=23819686
#Tang2013 pmid=23741390
#Ravalason2009 pmid=19414054
#Han2013 pmid=23503312
#Lawson1994 pmid=8107143
#Ficko20092 pmid=19422833
#Lammerts2007 pmid=17095014
#Lammerts2005 pmid=15501830
#Kellett1990 pmid=2125205
#Ferriera1990 pmid=2115772
#Ferriera1993 pmid=8373350
#Svensson1989 pmid=2481445
#Shallus2008 pmid=18524852
#Armenta2017 pmid=28547780
#Adams2008 pmid=18716000
#Freelove2001 pmid=11560933
#Poole1992 pmid=1490597
#Morag1995 pmid=7646033
#Taylor2014 pmid=25102772
#Boraston2006 pmid=16230347
#Lewis1986 pmid=3745156
#Endo1987 pmid=3036799
#Weis1992 pmid=1436090
#Veelders2010 pmid=21149680
#Maestre-Reyna2012 pmid=23035251
#Ielasi2012 pmid=22349222
#Lammerts2011 pmid=21565699
#Meekins2014 pmid=24799671
#Rigden2004 pmid=15236739
#Yoshida2010 pmid=20662765
#Larsbrink2011 pmid=21426303
#Tailford2007 pmid=17287210
#Ficko-Blean2012 pmid=22858095
#McLean2002 pmid=12191997
#Jervis1997 pmid=9295354
#Ficko-Blean2006 pmid=16990278
#king2014 pmid=25210925
</biblio>

[[Category:Definitions and explanations]]

User:Shinya Fushinobu

2017-06-23T03:52:58Z

Shinya Fushinobu:

File:Fushinobu3.jpg

2017-06-23T03:44:26Z

Shinya Fushinobu: He smiles.

He smiles.

User:Shinya Fushinobu

2016-08-12T12:44:20Z

Shinya Fushinobu:

[[Image:Fushinobu2.jpg|250px|right]]

I am a Professor at [http://enzyme13.bt.a.u-tokyo.ac.jp/index-e.html Laboratory of Enzymology] in Department of Biotechnology, [http://www.a.u-tokyo.ac.jp/english/index.html Graduate School of Agricultural and Life Sciences], [http://www.u-tokyo.ac.jp/index_e.html The University of Tokyo] located in Tokyo, Japan. Raised in [http://www.city.kure.hiroshima.jp/site/userguide/foreign.html Kure], Hiroshima, Japan. I obtained Ph.D degree in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern structure and function of enzymes, mainly those of Carbohydrate-Active enZymes. My home page is [http://enzyme13.bt.a.u-tokyo.ac.jp/fushi/index-e.html here]. I contributed to three-dimensional structure determination of

*[[GH1]] ''Phanerochaete chrysosporium'' β-glucosidase 1B (BGL1B) <cite>Nijikken2007</cite>
*[[GH1]] Metagenomic β-Glucosidase (Td2F2) <cite>Matsuzawa2016</cite>
*[[GH3]] ''Kluyveromyces marxianus'' β-glucosidase (''Km''BglI) <cite>Yoshida2010</cite>
*[[GH3]] ''Aspergillus aculeatus'' β-glucosidase (''Aa''BGL1) <cite>Suzuki2013</cite>
*[[GH8]] ''Bacillus halodurans'' reducing-end xylose-releasing exo-oligoxylanase (Rex) <cite>Fushinobu2005</cite>
*[[GH9]] ''Photobacterium profundum'' exo-β-D-glucosaminidase (PpGlcNase) <cite>Honda2016</cite>

*[[GH10]] ''Clostridium stercorarium'' xylanase B (XynB) <cite>Nishimoto2007</cite>
*[[GH11]] ''Aspergillus kawachii'' xylanase C (XynC) <cite>Fushinobu1998</cite>
*[[GH20]] ''Bifidobacterium bifidum'' lacto-''N''-biosidase (''Bb''LNBase) <cite>Ito2013</cite>
*[[GH26]] β-mannanase from a symbiotic protist of the termite ''Reticulitermes speratus'' (''Rs''Man26C) <cite>Tsukagoshi2014</cite>
*[[GH29]] ''Bifidobacterium longum'' subsp. ''infantis'' 1,3-1,4-α-L-fucosidase (''Bi''AfcB) <cite>Sakurama2012</cite>
*[[GH42]] ''Thermus thermophilus'' β-galactosidase (A4-β-Gal) '''Family First''' <cite>Hidaka2002</cite>
*[[GH45]] ''Phanerochaete chrysosporium'' endoglucanase (PcCel45A) <cite>Nakamura2015</cite>

*[[GH51]] ''Thermotoga maritima'' α-L-arabinofuranosidase (''Tm''-AFase) <cite>Im2012</cite>
*[[GH54]] ''Aspergillus kawachii'' α-L-arabinofuranosidase B (AkAbfB) '''Family First''' plus identification of [[CBM42]] <cite>Miyanaga2004</cite>
*[[GH55]] ''Phanerochaete chrysosporium'' β-1,3-glucanase (Lam55A) '''Family First''' <cite>Ishida2009</cite>
*[[GH57]] ''Thermococcus litoralis'' 4-α-glucanotransferase (TLGT) '''Family First''' <cite>Imamura2003</cite>
*[[GH65]] ''Caldicellulosiruptor saccharolyticus'' kojibiose phosphorylase (CsKP) <cite>Okada2013</cite>
*[[GH65]] ''Bacillus selenitireducens'' 2-''O''-α-glucosylglycerol phosphorylase (GGP) <cite>Touhara2014</cite>

*[[GH94]] ''Vibrio proteolyticus'' chitobiose phosphorylase (ChBP) '''Family First''' <cite>Hidaka2004</cite>
*[[GH94]] ''Cellvibrio gilvus'' cellobiose phosphorylase (CBP) <cite>Hidaka2006</cite>
*[[GH94]] ''Saccharophagus degradans'' cellobionic acid phosphorylase (CABP) <cite>Nam2015</cite>
*[[GH101]] ''Bifidobacterium longum'' endo-α-''N''-acetylgalactosaminidase (EngBF) <cite>Suzuki2009</cite>
*[[GH112]] ''Bifidobacterium longum'' galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) '''Family First''' <cite>Hidaka2009</cite>
*[[GH127]] ''Bifidobacterium longum'' β-L-arabinofuranosidase (HypBA1) '''Family First''' <cite>Ito2014</cite>
*[[GH130]] ''Listeria innocua'' β-1,2-mannobiose phosphorylase (Lin0857) <cite>Tsuda2015</cite>

*[[PL20]] ''Trichoderma reesei'' endo-β-1,4-glucuronan lyase (TrGL) '''Family First''' <cite>Konno2009</cite>
*[[CBM28]] in ''Clostridium josui'' Cel5A (''Cj''CBM28) <cite>Tsukimoto2010</cite>

----

<biblio>
#Nijikken2007 pmid=17376440
#Yoshida2010 pmid=20662765
#Suzuki2013 pmid=23537284
#Fushinobu2005 pmid=15718242
#Nishimoto2007 pmid=17383976
#Fushinobu1998 pmid=9930661
#Ito2013 pmid=23479733
#Tsukagoshi2014 pmid=24570006

#Sakurama2012 pmid=22451675
#Hidaka2002 pmid=12215416

#Miyanaga2004 pmid=15292273
#Ishida2009 pmid=19193645
#Imamura2003 pmid=12618437
#Okada2013 pmid=24255995

#Hidaka2004 pmid=15274915

#Hidaka2006 pmid=16646954
#Suzuki2009 pmid=19502354
#Hidaka2009 pmid=19124470
#Konno2009 pmid=19306878
#Tsukimoto2010 pmid=20159017
#Im2012 pmid=22313787

#Ito2014 pmid=24680821
#Touhara2014 pmid=24828502
#Nam2015 pmid=26041776
#Nakamura2015 pmid=26601228
#Tsuda2015 pmid=26632508
#Honda2016 pmid=26621872
#Matsuzawa2016 pmid=27092463

</biblio>

[[Category:Contributors|Fushinobu, Shinya]]

Carbohydrate Binding Module Family 28

2016-08-12T02:19:11Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM28.html
|}
</div>


== Ligand specificities ==
This module was first classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. All known CBM28s are so far derived from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or β-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.

== Structural Features ==
[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. Ca2+ ions in CBM28 and CBM17 are shown as green spheres in the ribbon representations (upper). Important residues in the cleft are colored yellow (aromatic), red (acidic), blue (basic), and green (neutral) on the molecular surfaces (lower). |frame|right]]

CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the concave face of the β-sandwich fold. A Ca2+ ion is bound on the back side of molecule. The Ca2+ ion is not involved in ligand binding but appears to play a structural stabilization role. These modules are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain in an open cleft. '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on the concave face (side) of the β-sandwich fold, not within the variable loop region ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

== Functionalities ==
CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>. They are exclusively associated with [[GH5]] endo-β-1,4-glucanases and a survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains. As a typical endo-type (Type B) CBM, CBM28s show the Ka values of 0.7-5.2 ×104 M-1 for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high-affinity (Ka = 9.9 ×105 M-1) and low-affinity (Ka = 2.1 ×104 M-1) cites <cite>Boraston2003</cite>. A novel application of CBM28 molecules was recently published where ''Bsp''CBM28 was used as a marker to identify amorphous regions in cellulose in photoactivated localization microscopy (PALM) studies <cite>Fox2013</cite>.

== Family Firsts ==
;First Identified
The first identified member is the C-terminal module in Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>

;First Structural Characterization
Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in apo form ([{{PDBlink}}1uww 1uww]) <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) ([{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite>.

== References ==
<biblio>
#Boraston2002 pmid=11743880
#Boraston2003 pmid=12427734
#Tsukimoto2010 pmid=20159017
#Notenboom2011 pmid=11733998
#Boraston2002-2 pmid=12079353
#Araki2009 pmid=19420681

#Fox2013 pmid=23563526
#Mosbah2002 pmid=12153043
#Jamal2004 pmid=15136030
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM028]]

User:Shinya Fushinobu

2016-08-12T02:01:07Z

Shinya Fushinobu:

[[Image:Fushinobu2.jpg|250px|right]]

I am a Professor at [http://enzyme13.bt.a.u-tokyo.ac.jp/index-e.html Laboratory of Enzymology] in Department of Biotechnology, [http://www.a.u-tokyo.ac.jp/english/index.html Graduate School of Agricultural and Life Sciences], [http://www.u-tokyo.ac.jp/index_e.html The University of Tokyo] located in Tokyo, Japan. Raised in [http://www.city.kure.hiroshima.jp/english/index.html Kure], Hiroshima, Japan. I obtained Ph.D degree in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern structure and function of enzymes, mainly those of Carbohydrate-Active enZymes. My home page is [http://enzyme13.bt.a.u-tokyo.ac.jp/fushi/index-e.html here]. I contributed to three-dimensional structure determination of

*[[GH1]] ''Phanerochaete chrysosporium'' β-glucosidase 1B (BGL1B) <cite>Nijikken2007</cite>
*[[GH1]] Metagenomic β-Glucosidase (Td2F2) <cite>Matsuzawa2016</cite>
*[[GH3]] ''Kluyveromyces marxianus'' β-glucosidase (''Km''BglI) <cite>Yoshida2010</cite>
*[[GH3]] ''Aspergillus aculeatus'' β-glucosidase (''Aa''BGL1) <cite>Suzuki2013</cite>
*[[GH8]] ''Bacillus halodurans'' reducing-end xylose-releasing exo-oligoxylanase (Rex) <cite>Fushinobu2005</cite>
*[[GH9]] ''Photobacterium profundum'' exo-β-D-glucosaminidase (PpGlcNase) <cite>Honda2016</cite>

*[[GH10]] ''Clostridium stercorarium'' xylanase B (XynB) <cite>Nishimoto2007</cite>
*[[GH11]] ''Aspergillus kawachii'' xylanase C (XynC) <cite>Fushinobu1998</cite>
*[[GH20]] ''Bifidobacterium bifidum'' lacto-''N''-biosidase (''Bb''LNBase) <cite>Ito2013</cite>
*[[GH26]] β-mannanase from a symbiotic protist of the termite ''Reticulitermes speratus'' (''Rs''Man26C) <cite>Tsukagoshi2014</cite>
*[[GH29]] ''Bifidobacterium longum'' subsp. ''infantis'' 1,3-1,4-α-L-fucosidase (''Bi''AfcB) <cite>Sakurama2012</cite>
*[[GH42]] ''Thermus thermophilus'' β-galactosidase (A4-β-Gal) '''Family First''' <cite>Hidaka2002</cite>
*[[GH45]] ''Phanerochaete chrysosporium'' endoglucanase (PcCel45A) <cite>Nakamura2015</cite>

*[[GH51]] ''Thermotoga maritima'' α-L-arabinofuranosidase (''Tm''-AFase) <cite>Im2012</cite>
*[[GH54]] ''Aspergillus kawachii'' α-L-arabinofuranosidase B (AkAbfB) '''Family First''' plus identification of [[CBM42]] <cite>Miyanaga2004</cite>
*[[GH55]] ''Phanerochaete chrysosporium'' β-1,3-glucanase (Lam55A) '''Family First''' <cite>Ishida2009</cite>
*[[GH57]] ''Thermococcus litoralis'' 4-α-glucanotransferase (TLGT) '''Family First''' <cite>Imamura2003</cite>
*[[GH65]] ''Caldicellulosiruptor saccharolyticus'' kojibiose phosphorylase (CsKP) <cite>Okada2013</cite>
*[[GH65]] ''Bacillus selenitireducens'' 2-''O''-α-glucosylglycerol phosphorylase (GGP) <cite>Touhara2014</cite>

*[[GH94]] ''Vibrio proteolyticus'' chitobiose phosphorylase (ChBP) '''Family First''' <cite>Hidaka2004</cite>
*[[GH94]] ''Cellvibrio gilvus'' cellobiose phosphorylase (CBP) <cite>Hidaka2006</cite>
*[[GH94]] ''Saccharophagus degradans'' cellobionic acid phosphorylase (CABP) <cite>Nam2015</cite>
*[[GH101]] ''Bifidobacterium longum'' endo-α-''N''-acetylgalactosaminidase (EngBF) <cite>Suzuki2009</cite>
*[[GH112]] ''Bifidobacterium longum'' galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) '''Family First''' <cite>Hidaka2009</cite>
*[[GH127]] ''Bifidobacterium longum'' β-L-arabinofuranosidase (HypBA1) '''Family First''' <cite>Ito2014</cite>
*[[GH130]] ''Listeria innocua'' β-1,2-mannobiose phosphorylase (Lin0857) <cite>Tsuda2015</cite>

*[[PL20]] ''Trichoderma reesei'' endo-β-1,4-glucuronan lyase (TrGL) '''Family First''' <cite>Konno2009</cite>
*[[CBM28]] in ''Clostridium josui'' Cel5A (''Cj''CBM28) <cite>Tsukimoto2010</cite>

----

<biblio>
#Nijikken2007 pmid=17376440
#Yoshida2010 pmid=20662765
#Suzuki2013 pmid=23537284
#Fushinobu2005 pmid=15718242
#Nishimoto2007 pmid=17383976
#Fushinobu1998 pmid=9930661
#Ito2013 pmid=23479733
#Tsukagoshi2014 pmid=24570006

#Sakurama2012 pmid=22451675
#Hidaka2002 pmid=12215416

#Miyanaga2004 pmid=15292273
#Ishida2009 pmid=19193645
#Imamura2003 pmid=12618437
#Okada2013 pmid=24255995

#Hidaka2004 pmid=15274915

#Hidaka2006 pmid=16646954
#Suzuki2009 pmid=19502354
#Hidaka2009 pmid=19124470
#Konno2009 pmid=19306878
#Tsukimoto2010 pmid=20159017
#Im2012 pmid=22313787

#Ito2014 pmid=24680821
#Touhara2014 pmid=24828502
#Nam2015 pmid=26041776
#Nakamura2015 pmid=26601228
#Tsuda2015 pmid=26632508
#Honda2016 pmid=26621872
#Matsuzawa2016 pmid=27092463

</biblio>

[[Category:Contributors|Fushinobu, Shinya]]

File:Fushinobu2.jpg

2016-08-12T02:00:26Z

Shinya Fushinobu: Shinya Fushinobu uploaded a new version of File:Fushinobu2.jpg

He gets older.

File:Fushinobu2.jpg

2016-08-12T01:59:40Z

Shinya Fushinobu: He gets older.

He gets older.

User:Shinya Fushinobu

2016-08-12T01:44:08Z

Shinya Fushinobu:

[[Image:Fushinobu.jpg|200px|right]]

I am a Professor at [http://enzyme13.bt.a.u-tokyo.ac.jp/index-e.html Laboratory of Enzymology] in Department of Biotechnology, [http://www.a.u-tokyo.ac.jp/english/index.html Graduate School of Agricultural and Life Sciences], [http://www.u-tokyo.ac.jp/index_e.html The University of Tokyo] located in Tokyo, Japan. Raised in [http://www.city.kure.hiroshima.jp/english/index.html Kure], Hiroshima, Japan. I obtained Ph.D degree in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern structure and function of enzymes, mainly those of Carbohydrate-Active enZymes. My home page is [http://enzyme13.bt.a.u-tokyo.ac.jp/fushi/index-e.html here]. I contributed to three-dimensional structure determination of

*[[GH1]] ''Phanerochaete chrysosporium'' β-glucosidase 1B (BGL1B) <cite>Nijikken2007</cite>
*[[GH1]] Metagenomic β-Glucosidase (Td2F2) <cite>Matsuzawa2016</cite>
*[[GH3]] ''Kluyveromyces marxianus'' β-glucosidase (''Km''BglI) <cite>Yoshida2010</cite>
*[[GH3]] ''Aspergillus aculeatus'' β-glucosidase (''Aa''BGL1) <cite>Suzuki2013</cite>
*[[GH8]] ''Bacillus halodurans'' reducing-end xylose-releasing exo-oligoxylanase (Rex) <cite>Fushinobu2005</cite>
*[[GH9]] ''Photobacterium profundum'' exo-β-D-glucosaminidase (PpGlcNase) <cite>Honda2016</cite>

*[[GH10]] ''Clostridium stercorarium'' xylanase B (XynB) <cite>Nishimoto2007</cite>
*[[GH11]] ''Aspergillus kawachii'' xylanase C (XynC) <cite>Fushinobu1998</cite>
*[[GH20]] ''Bifidobacterium bifidum'' lacto-''N''-biosidase (''Bb''LNBase) <cite>Ito2013</cite>
*[[GH26]] β-mannanase from a symbiotic protist of the termite ''Reticulitermes speratus'' (''Rs''Man26C) <cite>Tsukagoshi2014</cite>
*[[GH29]] ''Bifidobacterium longum'' subsp. ''infantis'' 1,3-1,4-α-L-fucosidase (''Bi''AfcB) <cite>Sakurama2012</cite>
*[[GH42]] ''Thermus thermophilus'' β-galactosidase (A4-β-Gal) '''Family First''' <cite>Hidaka2002</cite>
*[[GH45]] ''Phanerochaete chrysosporium'' endoglucanase (PcCel45A) <cite>Nakamura2015</cite>

*[[GH51]] ''Thermotoga maritima'' α-L-arabinofuranosidase (''Tm''-AFase) <cite>Im2012</cite>
*[[GH54]] ''Aspergillus kawachii'' α-L-arabinofuranosidase B (AkAbfB) '''Family First''' plus identification of [[CBM42]] <cite>Miyanaga2004</cite>
*[[GH55]] ''Phanerochaete chrysosporium'' β-1,3-glucanase (Lam55A) '''Family First''' <cite>Ishida2009</cite>
*[[GH57]] ''Thermococcus litoralis'' 4-α-glucanotransferase (TLGT) '''Family First''' <cite>Imamura2003</cite>
*[[GH65]] ''Caldicellulosiruptor saccharolyticus'' kojibiose phosphorylase (CsKP) <cite>Okada2013</cite>
*[[GH65]] ''Bacillus selenitireducens'' 2-''O''-α-glucosylglycerol phosphorylase (GGP) <cite>Touhara2014</cite>

*[[GH94]] ''Vibrio proteolyticus'' chitobiose phosphorylase (ChBP) '''Family First''' <cite>Hidaka2004</cite>
*[[GH94]] ''Cellvibrio gilvus'' cellobiose phosphorylase (CBP) <cite>Hidaka2006</cite>
*[[GH94]] ''Saccharophagus degradans'' cellobionic acid phosphorylase (CABP) <cite>Nam2015</cite>
*[[GH101]] ''Bifidobacterium longum'' endo-α-''N''-acetylgalactosaminidase (EngBF) <cite>Suzuki2009</cite>
*[[GH112]] ''Bifidobacterium longum'' galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) '''Family First''' <cite>Hidaka2009</cite>
*[[GH127]] ''Bifidobacterium longum'' β-L-arabinofuranosidase (HypBA1) '''Family First''' <cite>Ito2014</cite>
*[[GH130]] ''Listeria innocua'' β-1,2-mannobiose phosphorylase (Lin0857) <cite>Tsuda2015</cite>

*[[PL20]] ''Trichoderma reesei'' endo-β-1,4-glucuronan lyase (TrGL) '''Family First''' <cite>Konno2009</cite>
*[[CBM28]] in ''Clostridium josui'' Cel5A (''Cj''CBM28) <cite>Tsukimoto2010</cite>

----

<biblio>
#Nijikken2007 pmid=17376440
#Yoshida2010 pmid=20662765
#Suzuki2013 pmid=23537284
#Fushinobu2005 pmid=15718242
#Nishimoto2007 pmid=17383976
#Fushinobu1998 pmid=9930661
#Ito2013 pmid=23479733
#Tsukagoshi2014 pmid=24570006

#Sakurama2012 pmid=22451675
#Hidaka2002 pmid=12215416

#Miyanaga2004 pmid=15292273
#Ishida2009 pmid=19193645
#Imamura2003 pmid=12618437
#Okada2013 pmid=24255995

#Hidaka2004 pmid=15274915

#Hidaka2006 pmid=16646954
#Suzuki2009 pmid=19502354
#Hidaka2009 pmid=19124470
#Konno2009 pmid=19306878
#Tsukimoto2010 pmid=20159017
#Im2012 pmid=22313787

#Ito2014 pmid=24680821
#Touhara2014 pmid=24828502
#Nam2015 pmid=26041776
#Nakamura2015 pmid=26601228
#Tsuda2015 pmid=26632508
#Honda2016 pmid=26621872
#Matsuzawa2016 pmid=27092463

</biblio>

[[Category:Contributors|Fushinobu, Shinya]]

User:Wataru Saburi

2015-03-18T12:55:39Z

Shinya Fushinobu:

[[Image:Saburi2.jpg|200px|right]]

'''Wataru Saburi''' is an assistant professor at Laboratory of Biochemistry in Research Faculty of Agriculture, Hokkaido University (Sapporo, Japan). He obtained Ph. D from Graduate School of Agriculture, Hokkaido University in 2006, under the supervision of Professor Atsuo Kimura. He joined the Research Institute of Nihon Shokuhin Kako Co. Ltd. as a researcher (2006-2010), and developed functional oligosaccharides produced from starch. His research interests are structures and functions of carbohydrate active enzymes and efficient synthesis of functional oligosaccharides. He has studied about

* [[GH1]] rice β-glucosidase <cite>Himeno2013</cite>
* [[GH13]] ''Bacillus'' sp. AAH-31 α-amylase <cite>Kim2012 Saburia2013</cite>
* [[GH13]] ''Streptococcus mutans'' dextran glucosidase <cite>Saburi2006 Saburi2007 Hondoh2008 Kobayashi2011 Saburib2013 Saburi2015b Kobayashi2015</cite>
* [[GH13]] ''Halomonas'' sp. H11 α-glucosidase <cite>Ojima2012</cite>
* [[GH13]] ''Bacillus clarkii'' γ-cyclodextrinase <cite>Nakagawa2008</cite>
* [[GH31]] ''Bacillus'' sp. AHU 2001 α-glucosidase BspAG31A <cite>Saburi2014</cite>
* [[GH94]] ''Ruminococcus albus'' cellobiose phosphorylase <cite>Hamura2012 Hamura2013</cite>
* [[GH94]] ''Ruminococcus albus'' cellodextrin phosphorylase <cite>Sawano2013</cite>
* [[GH130]] ''Ruminococcus albus'' 4-''O''-β-mannosylglucose phosphorylase (RaMP1) <cite>Kawahara2012</cite>
* [[GH130]] ''Rhodothermus marinus'' 4-''O''-β-mannosylglucose phosphorylase <cite>Jaito2014</cite>

* [[GH130]] ''Cellvibrio vulgaris'' 4-''O''-β-mannosylglucose phosphorylase <cite>Saburi2015</cite>
* [[GH130]] ''Ruminococcus albus'' β-1,4-mannooligosaccharide phosphorylase (RaMP2) <cite>Kawahara2012</cite>

----

<biblio>
#Himeno2013 pmid=23649259
#>Kim2012 pmid=22785486
#>Saburia2013 pmid=24018662
#>Saburi2006 pmid=16503208
#>Saburi2007 pmid=17768352
#>Hondoh2008 pmid=18395742
#>Kobayashi2011 pmid=21821929
#>Saburib2013 pmid=24052257
#>Ojima2012 pmid=22226947
#>Nakagawa2008 pmid=18824139
#>Saburi2014 pmid=25450253
#>Hamura2012 pmid=22484959
#>Hamura2013 pmid=23845516
#>Sawano2013 pmid=23802549
#>Kawahara2012 pmid=23093406
#>Jaito2014 pmid=25036679

#>Saburi2015 pmid=25704402

#>Saburi2015b pmid=25728274

#>Kobayashi2015 pmid=25595454
</biblio>


[[Category:Contributors|Saburi,Wataru]]

Glycoside Hydrolase Family 130

2015-03-17T03:23:00Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Wataru Saburi^^^
* [[Responsible Curator]]: ^^^Haruhide Mori^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH130'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH130.html
|}
</div>


== Substrate specificities ==
[[GH130]] contains phosphorylases catalyzing the phosphorolysis of β-mannosidic linkage at the non-reducing end of substrates. 4-O-β-D-Mannosyl-D-glucose phosphorylase (EC [{{EClink}}2.4.1.281 2.4.1.281]), β-1,4-mannooligosaccharide phosphorylase (EC [{{EClink}}2.4.1.319 2.4.1.319]), 1,4-β-mannosyl-''N''-acetylglucosamine phosphorylase (EC [{{EClink}}2.4.1.320 2.4.1.320]), 1,2-β-oligomannan phosphorylase, and β-1,2-mannnobiose phosphorylase are members of this family. A GH130 mannoside phosphorylase, unknown human gut bacterium mannoside phosphorylase (UhgbMP), discovered by functional metagenomics of the human gut microbiota, phosphorolyzes 4-O-β-D-mannosyl-N,N'-diacetylchitobiose, and exhibits higher synthetic activity to ''N'',''N'''-diacetylchitobiose as an acceptor substrate than ''N''-acetyl-D-glucosamine <cite>Ladeveze2013</cite>.
== Kinetics and Mechanism ==
GH130 phosphorylases phosphorolyze β-mannosidic linkage at the non-reducing end of substrates with net inversion of anomeric configuration. Senoura et al. <cite>Senoura2011</cite> demonstrated that 4-''O''-β-D-mannosyl-D-glucose phosphorylase from ''Bacteroides fragilis'' (BfMGP) produces α-mannose 1-phosphate and glucose from 4-''O''-β-D-mannosyl-D-glucose and inorganic phosphate. A unique reaction mechanism of GH130 enzymes has been proposed on the basis of the three-dimensional strucuture of BfMGP <cite>Nakae2013</cite>. In contrast to known inverting glycoside phosphorylases, whose general acid catalyst directly donates a proton to glycosidic oxygen, the catalytic Asp of GH130 enzymes (Asp131 in BfMGP) donates a proton to O3 of mannosyl group bound to subsite -1, and a proton is tranferred to the glycosidic oxygen from 3OH group of the mannosyl residue. Inorganic phosphate attacks C1 of the mannosyl residue at the non-reducing end of substrate and α-mannose 1-phosphate is generated.

== Catalytic Residues ==
Ladevèze et al. <cite>Ladeveze2013</cite> compared 369 protein sequences of GH130 members and selected Asp104, Glu273, and Asp304 of UhgbMP as putative catalytic amino acid residues. Substitution of these acidic amino acid residues resulted in large reduction of enzyme activity. Especially, the D104N mutation comletely abolished the activity. Consistent with this result, three dimensional structure analysis demonstrated that only Asp131 of BfMGP, corresponding to Asp104 of UhgbMP, is situated near the scicile glycosidic oxigen <cite>Nakae2013</cite>. However, this Asp appeared to be too distant from the the scicile glycosidic oxigen for a direct protonation. Thus the proton relay mechanism described above has been posturated.

== Three-dimensional structures ==
Three-dimensinal structure of BfMGP has been first reported as a characterized enzyme <cite>Nakae2013</cite>. The structures of BfMGP in complex with phosphate; 4-''O''-β-D-mannosyl-D-glucose and phosphate; mannose, glucose, and phosphate; and α-mannose 1-phosphate were determined. The structure of catalytic domain of BfMGP is a five-bladed β-propeller fold. BfMGP forms a homohexamer. It has long α-helices at the N- and C-termini, and these structure are predicted to be responsible for the quaternary structure formation.

== Family Firsts ==
;First stereochemistry determination: BfMGP <cite>Senoura2011</cite>
;First general acid residue identification: BfMGP <cite>Nakae2013</cite>
;First sequence identification: BfMGP <cite>Senoura2011</cite>

: Ruminococcus albus β-1,4-mannooligosaccharide phosphorylase <cite>Kawahara2012</cite>

: Bacteroides thetaiotaomicron 4-O-β-D-Mannosyl-D-glucose phosphorylase <cite>Nihira2013</cite>

: Thermoanaerobacter sp. X-514 1,2-β-oligomannan phosphorylase <cite>Chiku2014</cite>

: Thermoanaerobacter sp. X-514 β-1,2-mannnobiose phosphorylase <cite>Chiku2014</cite>

;First 3-D structure: BfMGP <cite>Nakae2013</cite>

== References ==
<biblio>
#Ladeveze2013 pmid=24043624

#Senoura2011 pmid=21539815

#Nakae2013 pmid=23954514

#Kawahara2012 pmid=23093406

#Nihira2013 pmid=23943617
#Chiku2014 pmid=25500577

</biblio>

[[Category:Glycoside Hydrolase Families|GH130]]

Glycoside Hydrolase Family 123

2015-03-17T02:59:14Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Tomomi Sumida^^^
* [[Responsible Curator]]: ^^^Tomomi Sumida^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH123'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|probably retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH123.html
|}
</div>


== Substrate specificities ==

The [[glycoside hydrolases]] family 123 contains β-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]) that degrade glycosphingolipids. These enzymes specifically hydrolyze the non-reducing terminal β-GalNAc linkage, but not β-GlcNAc linkage. The β-''N''-acetylgalactosaminidase (EC [{{EClink}}3.2.1.53 3.2.1.53]) is distinguished from β-hexosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) or β-''N''-acetylglucosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) because the β-''N''-acetylgalactosaminidase is specific to β-GalNAc linkage while β-''N''-acetylglucosaminidase is specific to β-GlcNAc linkage. β-Hexosaminidase hydrolyzes both β-GlcNAc and β-GalNAc linkages at non-reducing terminus. NgaP, ''N''-acetylgalactosaminidase from ''Paenibacillus'' sp., is the first cloned β-''N''-acetylgalactosaminidase and its primary structure is not similar to any glycoside hydrolases reported so far <cite>SumidaJBC2011</cite>, and, thus, this family is created.
The recombinant NgaP hydrolyzes ''p''NP-β-GalNAc but not ''p''NP-β-GlcNAc, ''p''NP-β-Gal, ''p''NP-α-GalNAc or other ''p''NP-glycosides, indicating that NgaP is a typical β-''N''-acetylgalactosaminidase.

== Kinetics and Mechanism ==

[[Glycoside hydrolases]] belonging to [[GH18]], [[GH20]] and [[GH85]] cleave the sugar residues containing C2-acetamide group such as β-GlcNAc and β-GalNAc through substrate-assisted catalysis involving [[neighboring group participation]]. Since NgaP hydrolyzes the β-GalNAc linkage, NgaP is proposed to use substrate-assisted catalysis. A comparison of secondary structure of NgaP with that of other enzymes that utilize substrate-assisted catalysis suggested that Glu608 and Asp607 of NgaP functions as a proton donor and a stabilizer of the 2-acetamide group of the β-GalNAc at the active site. Point mutation analysis confirmed that Glu608 and Asp607 are integral for the activity of NgaP. GalNAc-thiazoline, a structural analog of the oxazolinium intermediate of [[neighboring group participation]], was found to competitively inhibit the activity of NgaP. These results indicate that NgaP hydrolyzes the terminal β-GalNAc linkage through substrate-assisted catalysis.

== Catalytic Residues ==
Point mutation analysis suggested that Glu608 and Asp607 functions as a proton donor a stabilizer of the 2-acetamide group of the substrate in NgaP.

== Three-dimensional structures ==
Unknown

== Family Firsts ==
;First stereochemistry determination:
;First catalytic nucleophile identification:

The carbonyl oxygen of the C-2 acetamide group of the substrate behaves as a catalytic nucleophile.
;First general acid/base residue identification:

Site-directed mutagenesis indicated that Glu608 is an essential amino acid for the catalytic reaction in NgaP.
;First 3-D structure:
Not known

== References ==

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>
[[Category:Glycoside Hydrolase Families|GH123]]

Glycoside Hydrolase Family 123

2015-03-17T02:46:22Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Tomomi Sumida^^^
* [[Responsible Curator]]: ^^^Tomomi Sumida^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH123'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|probably retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH123.html
|}
</div>


== Substrate specificities ==

The [[glycoside hydrolases]] family 123 contains β-''N''-acetylgalactosaminidases (EC [{{EClink}}3.2.1.53 3.2.1.53]). These enzymes specifically hydrolyze the non-reducing terminal β-GalNAc linkage, but not β-GlcNAc linkage. The β-''N''-acetylgalactosaminidase (EC [{{EClink}}3.2.1.53 3.2.1.53]) is distinguished from β-hexosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) or β-''N''-acetylglucosaminidase (EC [{{EClink}}3.2.1.52 3.2.1.52]) because the β-''N''-acetylgalactosaminidase is specific to β-GalNAc linkage while β-''N''-acetylglucosaminidase is specific to β-GlcNAc linkage. β-Hexosaminidase hydrolyzes both β-GlcNAc and β-GalNAc linkages at non-reducing terminus. NgaP, ''N''-acetylgalactosaminidase from ''Paenibacillus'' sp., is the first cloned β-''N''-acetylgalactosaminidase and its primary structure is not similar to any glycoside hydrolases reported so far <cite>SumidaJBC2011</cite>, and, thus, this family is created.
The recombinant NgaP hydrolyzes ''p''NP-β-GalNAc but not ''p''NP-β-GlcNAc, ''p''NP-β-Gal, ''p''NP-α-GalNAc or other ''p''NP-glycosides, indicating that NgaP is a typical β-''N''-acetylgalactosaminidase.

== Kinetics and Mechanism ==

[[Glycoside hydrolases]] belonging to [[GH18]], [[GH20]] and [[GH85]] cleave the sugar residues containing C2-acetamide group such as β-GlcNAc and β-GalNAc through substrate-assisted catalysis involving [[neighboring group participation]]. Since NgaP hydrolyzes the β-GalNAc linkage, NgaP is proposed to use substrate-assisted catalysis. A comparison of secondary structure of NgaP with that of other enzymes that utilize substrate-assisted catalysis suggested that Glu608 and Asp607 of NgaP functions as a proton donor and a stabilizer of the 2-acetamide group of the β-GalNAc at the active site. Point mutation analysis confirmed that Glu608 and Asp607 are integral for the activity of NgaP. GalNAc-thiazoline, a structural analog of the oxazolinium intermediate of [[neighboring group participation]], was found to competitively inhibit the activity of NgaP. These results indicate that NgaP hydrolyzes the terminal β-GalNAc linkage through substrate-assisted catalysis.

== Catalytic Residues ==
Point mutation analysis suggested that Glu608 and Asp607 functions as a proton donor a stabilizer of the 2-acetamide group of the substrate in NgaP.

== Three-dimensional structures ==
Unknown

== Family Firsts ==
;First stereochemistry determination:
;First catalytic nucleophile identification:

The carbonyl oxygen of the C-2 acetamide group of the substrate behaves as a catalytic nucleophile.
;First general acid/base residue identification:

Site-directed mutagenesis indicated that Glu608 is an essential amino acid for the catalytic reaction in NgaP.
;First 3-D structure:
Not known

== References ==

<biblio>

#SumidaJBC2011 pmid=21297160

</biblio>
[[Category:Glycoside Hydrolase Families|GH123]]

Glycoside Hydrolase Family 127

2014-09-11T05:15:42Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: ^^^Kiyotaka Fujita^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH127'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH127.html
|}
</div>


== Substrate specificities ==
This family of [[glycoside hydrolases]] contains β-L-arabinofuranosidase activity, which was established for HypBA1 from ''Bifidobacterium longum'' JCM 1217 <cite>Fujita2011B</cite>. HypBA1 released L-arabinose from the following saccharides and amino acid glycoconjugates, but not from from hydroxyproline-rich glycoproteins (HRGPs) such as carrot extensin and potato lectin:
* Ara''f''β1-2Ara''f'' (β-Ara2, a product of the [[GH121]] β-L-arabinobiosidase from ''B. longum'' JCM 1217 <cite>Fujita2011A</cite>)
* Ara''f''β-hydroxyproline (Ara-Hyp)
* Ara''f''β1-2Ara''f''β-Hyp (Ara2-Hyp)
* Ara''f''β1-2Ara''f''β1-2Ara''f''β-hyp (Ara3-Hyp)
* methyl β-L-arabinofuranoside
* Ara''f''β1-2Ara''f''β-Me

The members of GH127 are also members of the [http://pfam.sanger.ac.uk/family/DUF1680 Pfam DUF1680 family], which is conserved in many species of bacteria, actinomycetes, fungi, and plants. Establishment of GH127 by biochemical analysis thus resolves the "domain of unknown function" status of this PFAM family.

== Kinetics and Mechanism ==
HypBA1 is a [[retaining]] enzyme. The stereochemical course of the reaction was shown by transglycosylation activity toward 1-alkanols, such as methanol, and produced methyl β-L-arabinofuranoside was identified by 1H-NMR and 13C-NMR analysis <cite>Fujita2011B</cite>.

== Catalytic Residues ==
In the crystal structure of HypBA1, a Zn2+ ion was bound to the active site <cite>Ito2014</cite>. A cysteine residue (Cys417), which is involved in the coordination of the Zn2+, was suggested to act as the nucleophile. Glu322 is possibly the acid/base catalyst. A possible reaction mechanism involving the cysteine residue as the nucleophile was suggested based on crystal structures, site-directed mutagenesis, some biochemical analysis, and quantum mechanical calculations <cite>Ito2014</cite>.

== Three-dimensional structures ==
HypBA1 from ''B. longum'' JCM 1217 <cite>Ito2014</cite>. It consists of a catalytic (α/α)6 barrel domain and two additional β-sandwich domains.

== Family Firsts ==
;First stereochemistry determination: This was determined with HypBA1 enzyme by measurement of glycosyl transfer reactions to methanol and the 1H-NMR and13C-NMR spectra <cite>Fujita2011B</cite>.
;First [[catalytic nucleophile]] identification:
;First [[general acid/base]] residue identification:
;First 3-D structure: HypBA1 from ''B. longum'' JCM 1217 by X-ray crystallography <cite>Ito2014</cite>.

== References ==
<biblio>
#Fujita2011A pmid=21149454
#Fujita2011B pmid=21914802
#Ito2014 pmid=24680821
</biblio>

[[Category:Glycoside Hydrolase Families|GH127]]

Polysaccharide Lyase Family 20

2014-09-11T04:47:05Z

Shinya Fushinobu: /* Substrate specificities */

{{CuratorApproved}}
* [[Author]]: ^^^Naotake Konno^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL20'''
|-
|'''3D Structure'''
|β-jelly roll
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|none
|-
|'''Active site residues'''
|unknown
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL20.html
|}
</div>


== Substrate specificities ==
Polysaccharide lyases of family 20 cleave β-1,4 linkages in polyglucuronate (β-1,4-glucuronan lyase; EC 4.2.2.14). The first PL20 enzyme was cloned from filamentous fungus ''Trichoderma reesei'' (TrGL) <cite>Konno2009a</cite>. TrGL was highly specific for β-1,4-glucuronan prepared from regenerated cellulose by 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO)-mediated oxidation (cellouronate).
Polyglucuronate is a minor polysaccharide compared with other polyuronates. But β-1,4-glucuronan structures are found in water-soluble polysaccharides from bacteria, fungi, and algae.

== Kinetics and Mechanism ==
TrGL has been characterized as a β-1,4-glucuronan lyase; TrGL catalyzed endolytic depolymerization of β-1,4-glucuronan by β-elimination <cite>Konno2009a</cite>. The enzyme was most active at pH 6.5 and 50°C, and its activity and thermostability increased in the presence of calcium ions.

== Catalytic Residues ==
There are approximately 40 completely conserved amino-acid residues in PL20 members <cite>Konno2009b</cite>. Possible catalytic residues have been predicted based on structural comparison between TrGL and PL7 alginate lyase A1–II’ <cite>Konno2009b Ogura2008</cite>. The charge neutralizer, the catalytic base, and the catalytic acid in TrGL are predicted to be Gln91, His53 and Tyr200, respectively. However, in order to clarify the substrate recognition mechanism and the identity of the catalytic residues of PL20, further studies will be required.

== Three-dimensional structures ==
[[Image:PL20.png|'''Figure 1:''' PL20 glucuronan lyase from ''Trichoderma reesei'' (2ZZJ).|frame|right]]
The ligand-free structure of TrGL was the first PL20 structure to be reported ('''Figure 1''', PDB ID [{{PDBlink}}2zzj 2zzj], 1.8 Å resolution) <cite>Konno2009b</cite>. TrGL has a typical β-jelly roll fold. A calcium binding site, which appears to contribute to the stability, was found at a position far from the cleft. However, no calcium binding site in the cleft has been identified.

== Family Firsts ==
;First catalytic activity: TrGl from ''Trichoderma reesei'' <cite>Konno2009a</cite>.
;First 3-D structure: TrGl from ''Trichoderma reesei'' <cite>Konno2009b</cite>.

== References ==
<biblio>
#Konno2009a pmid=18978091
#Konno2009b pmid=19306878
#Ogura2008 pmid=18514736
</biblio>

[[Category:Polysaccharide Lyase Families|PL020]]

Polysaccharide Lyase Family 20

2014-09-11T04:42:02Z

Shinya Fushinobu: /* Substrate specificities */

{{CuratorApproved}}
* [[Author]]: ^^^Naotake Konno^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL20'''
|-
|'''3D Structure'''
|β-jelly roll
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|none
|-
|'''Active site residues'''
|unknown
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL20.html
|}
</div>


== Substrate specificities ==
Polysaccharide lyases of family 20 cleave β-1,4 linkages in polyglucuronate (β-1,4-glucuronan lyase; EC 4.2.2.14). The first PL20 enzyme was cloned from filamentous fungus ''Trichoderma reesei'' (TrGL) <cite>Konno2009a</cite>. TrGL was highly specific for β-1,4-glucuronan prepared from regenerated cellulose by 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO)-mediated oxidation (cellouronate).
Polyglucuronate (glucuronan) is a minor polysaccharide compared with other polyuronates. But β-1,4-glucuronan structures are found in water-soluble polysaccharides from bacteria, fungi, and algae.

== Kinetics and Mechanism ==
TrGL has been characterized as a β-1,4-glucuronan lyase; TrGL catalyzed endolytic depolymerization of β-1,4-glucuronan by β-elimination <cite>Konno2009a</cite>. The enzyme was most active at pH 6.5 and 50°C, and its activity and thermostability increased in the presence of calcium ions.

== Catalytic Residues ==
There are approximately 40 completely conserved amino-acid residues in PL20 members <cite>Konno2009b</cite>. Possible catalytic residues have been predicted based on structural comparison between TrGL and PL7 alginate lyase A1–II’ <cite>Konno2009b Ogura2008</cite>. The charge neutralizer, the catalytic base, and the catalytic acid in TrGL are predicted to be Gln91, His53 and Tyr200, respectively. However, in order to clarify the substrate recognition mechanism and the identity of the catalytic residues of PL20, further studies will be required.

== Three-dimensional structures ==
[[Image:PL20.png|'''Figure 1:''' PL20 glucuronan lyase from ''Trichoderma reesei'' (2ZZJ).|frame|right]]
The ligand-free structure of TrGL was the first PL20 structure to be reported ('''Figure 1''', PDB ID [{{PDBlink}}2zzj 2zzj], 1.8 Å resolution) <cite>Konno2009b</cite>. TrGL has a typical β-jelly roll fold. A calcium binding site, which appears to contribute to the stability, was found at a position far from the cleft. However, no calcium binding site in the cleft has been identified.

== Family Firsts ==
;First catalytic activity: TrGl from ''Trichoderma reesei'' <cite>Konno2009a</cite>.
;First 3-D structure: TrGl from ''Trichoderma reesei'' <cite>Konno2009b</cite>.

== References ==
<biblio>
#Konno2009a pmid=18978091
#Konno2009b pmid=19306878
#Ogura2008 pmid=18514736
</biblio>

[[Category:Polysaccharide Lyase Families|PL020]]

Polysaccharide Lyase Family 20

2014-08-08T01:57:01Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: ^^^Naotake Konno^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL20'''
|-
|'''Mechanism'''
|β-elimination
|-
|'''Metal Cofactor'''
|calcium
|-
|'''Active site residues'''
|unknown
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL20.html
|}
</div>


== Substrate specificities ==
Polysaccharide lyases of family 20 cleave β-1,4 linkages in polyglucuronate (β-1,4-glucuronan lyase; EC 4.2.2.14). The first PL20 enzyme was cloned from filamentous fungus ''Trichoderma reesei'' (TrGL) <cite>Konno2009a</cite>. TrGL was highly specific for β-1,4-glucuronan prepared from regenerated cellulose by 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO)-mediated oxidation (cellouronate).

== Kinetics and Mechanism ==
A PL20 enzyme, TrGL, has been characterized as a β-1,4-glucuronan lyase. TrGL catalyzed depolymerization of β-1,4-glucuronan endolytically by β-elimination <cite>Konno2009a</cite>. The enzyme was most active at pH 6.5 and 50°C, and its activity and thermostability increased in the presence of calcium ions.

== Catalytic Residues ==
There are approximately 40 completely conserved amino-acid residues in the PL20 members <cite>Konno2009b</cite>. Possible catalytic residues has been predicted based on structural comparison between TrGL and PL7 alginate lyase A1–II’ <cite>Konno2009b</cite> <cite>Ogura2008</cite>. It seemed to be that the charge neutralizer, the catalytic base and the catalytic acid in the TrGL are Gln91, His53 and Tyr200, respectively. However, in order to clarify the substrate recognition mechanism and the identity of the catalytic residues of PL20, further studies will be required.

== Three-dimensional structures ==
[[Image:PL20.png|'''Figure 1:''' PL20 glucuronan lyase from ''Trichoderma reesei'' (2ZZJ).|frame|right]]
The ligand-free structure of the TrGL was the first PL20 structure to be reported ('''Figure 1''', PDB ID [{{PDBlink}}2zzj 2zzj], 1.8 Å resolution) <cite>Konno2009b</cite>. TrGL has a typical β-jelly roll fold. A calcium binding site, which appears to contribute to the stability, was found at a position far from the cleft. However, no calcium binding site in the cleft has been identified.

== Family Firsts ==
;First catalytic activity: TrGl from ''Trichoderma reesei'' <cite>Konno2009a</cite>.
;First 3-D structure: TrGl from ''Trichoderma reesei'' <cite>Konno2009b</cite>.

== References ==
<biblio>
#Konno2009a pmid=18978091
#Konno2009b pmid=19306878
#Ogura2008 pmid=18514736
</biblio>

[[Category:Polysaccharide Lyase Families|PL020]]

Polysaccharide Lyase Family 20

2014-08-07T13:13:11Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: ^^^Naotake Konno^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL20'''
|-
|'''Mechanism'''
|β-elimination
|-
|'''Metal Cofactor'''
|calcium
|-
|'''Active site residues'''
|unknown
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL20.html
|}
</div>


== Substrate specificities ==
Polysaccharide lyases of family 20 cleave β-1,4 linkages in polyglucuronate (β-1,4-glucuronan lyase; EC 4.2.2.14). The first PL20 enzyme was cloned from filamentous fungus ''Trichoderma reesei'' (TrGL) <cite>Konno2009a</cite>. TrGL was highly specific for β-1,4-glucuronan prepared from regenerated cellulose by 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO)-mediated oxidation (cellouronate).

== Kinetics and Mechanism ==
A PL20 enzyme, TrGL, has been characterized as a β-1,4-glucuronan lyase. TrGL catalyzed depolymerization of β-1,4-glucuronan endolytically by β-elimination <cite>Konno2009a</cite>. The enzyme was most active at pH 6.5 and 50 °C, and its activity and thermostability increased in the presence of calcium ions.

== Catalytic Residues ==
There are approximately 40 completely conserved amino-acid residues in the PL20 members <cite>Konno2009b</cite>. Possible catalytic residues has been predicted based on structural comparison between TrGL and PL7 alginate lyase A1–II’ <cite>Konno2009b</cite> <cite>Ogura2008</cite>. It seemed to be that the charge neutralizer, the catalytic base and the catalytic acid in the TrGL are Gln91, His53 and Tyr200, respectively. However, in order to clarify the substrate recognition mechanism and the identity of the catalytic residues of PL20, further studies will be required.

== Three-dimensional structures ==
[[Image:PL20.png|'''Figure 1:''' PL20 glucuronan lyase from ''Trichoderma reesei'' (2ZZJ).|frame|right]]
The ligand-free structure of the TrGL was the first PL20 structure to be reported (PDB ID [{{PDBlink}}2zzj 2zzj], 1.8 Å resolution) <cite>Konno2009b</cite>. TrGL has a typical β-jelly roll fold. A calcium binding site, which appears to contribute to the stability, was found at a position far from the cleft. However, no calcium binding site in the cleft has been identified.

== Family Firsts ==
;First catalytic activity: TrGl from ''Trichoderma reesei'' <cite>Konno2009a</cite>.
;First 3-D structure: TrGl from ''Trichoderma reesei'' <cite>Konno2009b</cite>.

== References ==
<biblio>
#Konno2009a pmid=18978091
#Konno2009b pmid=19306878
#Ogura2008 pmid=18514736
</biblio>

[[Category:Polysaccharide Lyase Families|PL020]]

File:PL20.png

2014-08-07T13:09:54Z

Shinya Fushinobu:

PL20 ''Trichoderma reesei'' glucuronan lyase

File:PL20.png

2014-08-07T13:09:11Z

Shinya Fushinobu: PL20 ''Trichoderma reesei glucuronan'' lyase

PL20 ''Trichoderma reesei glucuronan'' lyase

User:Naotake Konno

2014-08-07T09:54:03Z

Shinya Fushinobu:

----

[[File:Konno2.png|200px|right]]
Naotake Konno is an associate professor at Department of Applied Biological Chemistry, Utsunomiya University, Japan. He obtained Ph. D. from Graduate School of The University of Tokyo in 2009. He contributed isolation and enzymatic characterization of polysaccharide lyase and glycoside hydrolase belonging new families ([[PL20]] and [[GH128]]) <cite>Konno2009a</cite> <cite>Konno2009b</cite> <cite>Sakamoto2011</cite>. His research currently focuses on various carbohydrate-active enzymes acting on fungal cell walls, such as chitinases <cite>Konno2012</cite>, beta-1,3-glucanases <cite>Sakamoto2011</cite> and beta-1,6-glucanases <cite>Konno2011</cite>. Some of these enzymes are involved in fungal morphological changes.

----

<biblio>
#Konno2009a pmid=18978091
#Konno2009b pmid=19306878
#Sakamoto2011 pmid=21965406
#Konno2012 pmid=22656067
#Konno2011 pmid=21523473
</biblio>

[[Category:Contributors|Konno,Naotake]]

Carbohydrate Binding Module Family 28

2014-05-14T16:20:44Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM28.html
|}
</div>


== Ligand specificities ==
This module was firstly classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. Currently known CBM28s are solely from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or β-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.

== Structural Features ==
[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. Ca2+ ions in CBM28 and CBM17 are shown as green spheres in the ribbon representations (upper). Important residues in the cleft are colored yellow (aromatic), red (acidic), blue (basic), and green (neutral) on the molecular surfaces (lower). |frame|right]]

CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the β-sandwich fold. A Ca2+ ion is bound on the back side of molecule. The Ca2+ ion is not involved in ligand binding but appears to play a structural stabilization role.

CBM28s are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.

'''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on a face (side) of the β-sandwich fold, not on an apex/edge ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

== Functionalities ==
CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.

CBM28s are associated with endo-β-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.

As a typical endo-type (Type B) CBM, CBM28s show the Ka values of 0.7-5.2 ×104 M-1 for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high-affinity (Ka = 9.9 ×105 M-1) and low-affinity (Ka = 2.1 ×104 M-1) cites <cite>Boraston2003</cite>.

''Bsp''CBM28 was used as the most amorphous-specific CBM in a study of photoactivated localization microscopy (PALM) <cite>Fox2013</cite>.

== Family Firsts ==
;First Identified
The first identified member is the C-terminal module in Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>

;First Structural Characterization
Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in a ligand-free form ([{{PDBlink}}1uww 1uww]) <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) ([{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite>.

== References ==
<biblio>
#Boraston2002 pmid=11743880
#Boraston2003 pmid=12427734
#Tsukimoto2010 pmid=20159017
#Notenboom2011 pmid=11733998
#Boraston2002-2 pmid=12079353
#Araki2009 pmid=19420681

#Fox2013 pmid=23563526
#Mosbah2002 pmid=12153043
#Jamal2004 pmid=15136030
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM028]]

Carbohydrate Binding Module Family 42

2014-05-14T16:16:41Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM42.html
|}
</div>


== Ligand specificities ==
This module was originally identified as a non-catalytic xylan-binding domain in [[GH54]] α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51453 ''Trichoderma reesei''] PC-3-7 <cite>Nogawa1999</cite>. In 2004, it was found to be a CBM specific for an L-arabinofuranosyl group because L-arabinofuranose molecules were bound to a non-catalytic domain of [[GH54]] α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>. CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues, which are present in plant polysaccharides (hemicelluloses) such as arabinoxylan, arabinan, and arabinogalactan. Most of CBM42s are associated with α-L-arabinofuranosidases from fungi ([[GH54]]) or bacteria ([[GH43]]).

== Structural Features ==
[[Image:CBM42.png|'''Figure 1:''' CBM42 of α-L-arabinofuranosidase B from ''A. kawachii'' in complex with α-L-arabinofuranosyl-α-1,2-xylobiose (2D44). The α-domain is non-functional. |frame|right]]

CBM42s have a β-trefoil fold that is similar to [[CBM13]] and R(ricin)-type lectins ('''Figure 1'''). The module has a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one of the three subdomains sometimes loses its function due to mutations at critical residues for ligand binding.

CBM42s are typical [[Carbohydrate-binding_modules#Types|Type C CBMs]] that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans <cite>Miyanaga2006</cite>.

The binding sites are located at side pockets of the triangular structure of the β-trefoil fold. Residues important for the binding to a non-reducing end L-arabinofuranosyl group are as follows: an aspartate forming hydrogen bonds to the O2 and O3 hydroxyls, a histidine forming a hydrogen bond to the O5 hydroxyl, and two aromatic residues (tyrosine, tryptophan, or phenylalanine) stacking to the furanose sugar ('''Figure 1'''). They are D425, H416, Y417 and Y456 in the β-subdomain of AkAbfB and are conserved in functional CBM42 subdomains.

Several crystal structures including complex structures with compounds containing an L-arabinofuranosyl group are available. For example, AkAbfB (α-subdomain is non-functional) ([{{PDBlink}}1wd3 1wd3] [{{PDBlink}}1wd4 1wd4]) <cite>Miyanaga2004</cite>, ([{{PDBlink}}2d43 2d43] [{{PDBlink}}2d44 2d44]) <cite>Miyanaga2006</cite>; Exo-1,5-α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33903 ''Sreptomyces avermitilis''] (all subdomains are functional) ([{{PDBlink}}3akf 3akf] [{{PDBlink}}3akg 3akg] [{{PDBlink}}3akh 3akh] [{{PDBlink}}3aki 3aki]) <cite>Fujimoto2010</cite>; CBM42A in Cthe_0015 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1515 ''Clostridium thermocellum''] (β-subdomain is non-functional) ([{{PDBlink}}3kmv 3kmv]) <cite>Ribeiro2010</cite>.

== Functionalities ==
CBM42s are thought to target catalytic modules (usually α-L-arabinofuranosidases) to hemicelluloses that have L-arabinofuranosyl termini or branches. Mutations at the binding sites of CBM42 significantly reduced the catalytic activity toward natural polysaccharides in these enzymes, whereas the activity toward ''p''-nitrophenyl α-L-arabinofuranoside was not affected <cite>Miyanaga2006 Ribeiro2010</cite>.

CBM42s are commonly associated with α-L-arabinofuranosidases or exo-arabinanases of [[GH2]], [[GH43]], [[GH54]], [[GH93]], or non-classified GHs <cite>Ribeiro2010</cite>. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM42s are also associated with [[GH16]] or [[GH30]].

As a typical exo-type (Type C) CBM, the CBM42 in AkAbfB shows relatively low binding affinities to L-arabinofuranose-containing oligosaccharides with Ka values of 1~5 ×103 M-1. <cite>Miyanaga2006</cite>.

A CBM42 was used to create a chimeric enzyme with a feruloyl esterase <cite>Koseki2010</cite>.

== Family Firsts ==
;First Identified
The L-arabinofuranose-binding function of CBM42 was first suggested by crystallography of α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>.
;First Structural Characterization
The first structure of CBM42 was revealed in 2004 in the x-ray crystal structure of AkAbfB in complex with arabinose as a full-length structure with a catalytic [[GH54]] domain [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>.

== References ==
<biblio>
#Nogawa1999 pmid=10473402
#Miyanaga2004 pmid=15292273
#Miyanaga2006 pmid=16846393
#Fujimoto2010 pmid=20739278
#Ribeiro2010 pmid=20637315
#Koseki2010 pmid=19756576

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM042]]

Carbohydrate Binding Module Family 42

2014-05-14T16:13:50Z

Shinya Fushinobu: /* Structural Features */

{{CuratorApproved}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM42.html
|}
</div>


== Ligand specificities ==
This module was originally identified as a non-catalytic xylan-binding domain in [[GH54]] α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51453 ''Trichoderma reesei''] PC-3-7 <cite>Nogawa1999</cite>. In 2004, it was found to be a CBM specific for an L-arabinofuranosyl group because L-arabinofuranose molecules were bound to a non-catalytic domain of [[GH54]] α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>. CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues, which are present in plant polysaccharides (hemicelluloses) such as arabinoxylan, arabinan, and arabinogalactan. Most of CBM42s are associated with α-L-arabinofuranosidases from fungi ([[GH54]]) or bacteria ([[GH43]]).

== Structural Features ==
[[Image:CBM42.png|'''Figure 1:''' CBM42 of α-L-arabinofuranosidase B from ''A. kawachii'' in complex with α-L-arabinofuranosyl-α-1,2-xylobiose (2D44). The α-domain is non-functional. |frame|right]]

CBM42s have a β-trefoil fold that is similar to [[CBM13]] and R(ricin)-type lectins ('''Figure 1'''). The module has a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one of the three subdomains sometimes loses its function due to mutations at critical residues for ligand binding.

CBM42s are typical [[Carbohydrate-binding_modules#Types|Type C CBMs]] that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans <cite>Miyanaga2006</cite>.

The binding sites are located at side pockets of the triangular structure of the β-trefoil fold. Residues important for the binding to a non-reducing end L-arabinofuranosyl group are as follows: an aspartate forming hydrogen bonds to the O2 and O3 hydroxyls, a histidine forming a hydrogen bond to the O5 hydroxyl, and two aromatic residues (tyrosine, tryptophan, or phenylalanine) stacking to the furanose sugar ('''Figure 1'''). They are D425, H416, Y417 and Y456 in the β-subdomain of AkAbfB and are conserved in functional CBM42 subdomains.

Several crystal structures including complex structures with compounds containing an L-arabinofuranosyl group are available. For example, AkAbfB (α-subdomain is non-functional) ([{{PDBlink}}1wd3 1wd3] [{{PDBlink}}1wd4 1wd4]) <cite>Miyanaga2004</cite>, ([{{PDBlink}}2d43 2d43] [{{PDBlink}}2d44 2d44]) <cite>Miyanaga2006</cite>; Exo-1,5-α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33903 ''Sreptomyces avermitilis''] (all subdomains are functional) ([{{PDBlink}}3akf 3akf] [{{PDBlink}}3akg 3akg] [{{PDBlink}}3akh 3akh] [{{PDBlink}}3aki 3aki]) <cite>Fujimoto2010</cite>; CBM42A in Cthe_0015 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1515 ''Clostridium thermocellum''] (β-subdomain is non-functional) ([{{PDBlink}}3kmv 3kmv]) <cite>Ribeiro2010</cite>.

== Functionalities ==
* '''Functional role of CBM:''' CBM42s are thought to target catalytic modules (usually α-L-arabinofuranosidases) to hemicelluloses that have L-arabinofuranosyl termini or branches. Mutations at the binding sites of CBM42 significantly reduced the catalytic activity toward natural polysaccharides in these enzymes, whereas the activity toward ''p''-nitrophenyl α-L-arabinofuranoside was not affected <cite>Miyanaga2006 Ribeiro2010</cite>.
* '''Most Common Associated Modules:''' α-L-Arabinofuranosidases or exo-arabinanases of [[GH2]], [[GH43]], [[GH54]], [[GH93]], or non-classified GHs <cite>Ribeiro2010</cite>. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM42s are also associated with [[GH16]] or [[GH30]].
* '''Binding affinities:''' As a typical exo-type (Type C) CBM, the CBM42 in AkAbfB shows relatively low binding affinities to L-arabinofuranose-containing oligosaccharides with Ka values of 1~5 ×103 M-1. <cite>Miyanaga2006</cite>.
* '''Novel Applications:''' A CBM42 was used to create a chimeric enzyme with a feruloyl esterase <cite>Koseki2010</cite>.

== Family Firsts ==
;First Identified
The L-arabinofuranose-binding function of CBM42 was first suggested by crystallography of α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>.
;First Structural Characterization
The first structure of CBM42 was revealed in 2004 in the x-ray crystal structure of AkAbfB in complex with arabinose as a full-length structure with a catalytic [[GH54]] domain [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>.

== References ==
<biblio>
#Nogawa1999 pmid=10473402
#Miyanaga2004 pmid=15292273
#Miyanaga2006 pmid=16846393
#Fujimoto2010 pmid=20739278
#Ribeiro2010 pmid=20637315
#Koseki2010 pmid=19756576

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM042]]

Carbohydrate Binding Module Family 42

2014-05-14T09:12:49Z

Shinya Fushinobu: /* Structural Features */

{{CuratorApproved}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM42.html
|}
</div>


== Ligand specificities ==
This module was originally identified as a non-catalytic xylan-binding domain in [[GH54]] α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51453 ''Trichoderma reesei''] PC-3-7 <cite>Nogawa1999</cite>. In 2004, it was found to be a CBM specific for an L-arabinofuranosyl group because L-arabinofuranose molecules were bound to a non-catalytic domain of [[GH54]] α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>. CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues, which are present in plant polysaccharides (hemicelluloses) such as arabinoxylan, arabinan, and arabinogalactan. Most of CBM42s are associated with α-L-arabinofuranosidases from fungi ([[GH54]]) or bacteria ([[GH43]]).

== Structural Features ==
[[Image:CBM42.png|'''Figure 1:''' CBM42 of α-L-arabinofuranosidase B from ''A. kawachii'' in complex with α-L-arabinofuranosyl-α-1,2-xylobiose (2D44). The α-domain is non-functional. |frame|right]]

* '''Fold:''' CBM42s have a β-trefoil fold that is similar to [[CBM13]] and R(ricin)-type lectins ('''Figure 1'''). The module has a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one of the three subdomains sometimes loses its function due to mutations at critical residues for ligand binding.
* '''Type:''' CBM42s are typical [[Carbohydrate-binding_modules|Type C CBMs]] that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans <cite>Miyanaga2006</cite>.
* '''Features of ligand binding:''' The binding sites are located at side pockets of the triangular structure of the β-trefoil fold. Residues important for the binding to a non-reducing end L-arabinofuranosyl group are as follows: an aspartate forming hydrogen bonds to the O2 and O3 hydroxyls, a histidine forming a hydrogen bond to the O5 hydroxyl, and two aromatic residues (tyrosine, tryptophan, or phenylalanine) stacking to the furanose sugar ('''Figure 1'''). They are D425, H416, Y417 and Y456 in the β-subdomain of AkAbfB and are conserved in functional CBM42 subdomains.
* '''Available structures:''' Several crystal structures including complex structures with compounds containing an L-arabinofuranosyl group are available. For example, AkAbfB (α-subdomain is non-functional) ([{{PDBlink}}1wd3 1wd3] [{{PDBlink}}1wd4 1wd4]) <cite>Miyanaga2004</cite>, ([{{PDBlink}}2d43 2d43] [{{PDBlink}}2d44 2d44]) <cite>Miyanaga2006</cite>; Exo-1,5-α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33903 ''Sreptomyces avermitilis''] (all subdomains are functional) ([{{PDBlink}}3akf 3akf] [{{PDBlink}}3akg 3akg] [{{PDBlink}}3akh 3akh] [{{PDBlink}}3aki 3aki]) <cite>Fujimoto2010</cite>; CBM42A in Cthe_0015 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1515 ''Clostridium thermocellum''] (β-subdomain is non-functional) ([{{PDBlink}}3kmv 3kmv]) <cite>Ribeiro2010</cite>.

== Functionalities ==
* '''Functional role of CBM:''' CBM42s are thought to target catalytic modules (usually α-L-arabinofuranosidases) to hemicelluloses that have L-arabinofuranosyl termini or branches. Mutations at the binding sites of CBM42 significantly reduced the catalytic activity toward natural polysaccharides in these enzymes, whereas the activity toward ''p''-nitrophenyl α-L-arabinofuranoside was not affected <cite>Miyanaga2006 Ribeiro2010</cite>.
* '''Most Common Associated Modules:''' α-L-Arabinofuranosidases or exo-arabinanases of [[GH2]], [[GH43]], [[GH54]], [[GH93]], or non-classified GHs <cite>Ribeiro2010</cite>. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM42s are also associated with [[GH16]] or [[GH30]].
* '''Binding affinities:''' As a typical exo-type (Type C) CBM, the CBM42 in AkAbfB shows relatively low binding affinities to L-arabinofuranose-containing oligosaccharides with Ka values of 1~5 ×103 M-1. <cite>Miyanaga2006</cite>.
* '''Novel Applications:''' A CBM42 was used to create a chimeric enzyme with a feruloyl esterase <cite>Koseki2010</cite>.

== Family Firsts ==
;First Identified
The L-arabinofuranose-binding function of CBM42 was first suggested by crystallography of α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>.
;First Structural Characterization
The first structure of CBM42 was revealed in 2004 in the x-ray crystal structure of AkAbfB in complex with arabinose as a full-length structure with a catalytic [[GH54]] domain [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>.

== References ==
<biblio>
#Nogawa1999 pmid=10473402
#Miyanaga2004 pmid=15292273
#Miyanaga2006 pmid=16846393
#Fujimoto2010 pmid=20739278
#Ribeiro2010 pmid=20637315
#Koseki2010 pmid=19756576

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM042]]

Carbohydrate Binding Module Family 28

2014-05-14T09:09:21Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM28.html
|}
</div>


== Ligand specificities ==
This module was firstly classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. Currently known CBM28s are solely from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or β-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.

== Structural Features ==
[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. Ca2+ ions in CBM28 and CBM17 are shown as green spheres in the ribbon representations (upper). Important residues in the cleft are colored yellow (aromatic), red (acidic), blue (basic), and green (neutral) on the molecular surfaces (lower). |frame|right]]

* '''Fold:''' CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the β-sandwich fold. A Ca2+ ion is bound on the back side of molecule. The Ca2+ ion is not involved in ligand binding but appears to play a structural stabilization role.
* '''Type:''' CBM28s are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
* '''Features of ligand binding:''' '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on a face (side) of the β-sandwich fold, not on an apex/edge ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

== Functionalities ==
* '''Functional role of CBM:''' CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
* '''Most Common Associated Modules:''' Endo-β-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.
* '''Binding affinities:''' As a typical endo-type (Type B) CBM, CBM28s show the Ka values of 0.7-5.2 ×104 M-1 for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high-affinity (Ka = 9.9 ×105 M-1) and low-affinity (Ka = 2.1 ×104 M-1) cites <cite>Boraston2003</cite>.

* '''Novel Applications:''' ''Bsp''CBM28 was used as the most amorphous-specific CBM in a study of photoactivated localization microscopy (PALM) <cite>Fox2013</cite>.

== Family Firsts ==
;First Identified
The first identified member is the C-terminal module in Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>

;First Structural Characterization
Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in a ligand-free form ([{{PDBlink}}1uww 1uww]) <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) ([{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite>.

== References ==
<biblio>
#Boraston2002 pmid=11743880
#Boraston2003 pmid=12427734
#Tsukimoto2010 pmid=20159017
#Notenboom2011 pmid=11733998
#Boraston2002-2 pmid=12079353
#Araki2009 pmid=19420681

#Fox2013 pmid=23563526
#Mosbah2002 pmid=12153043
#Jamal2004 pmid=15136030
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM028]]

Carbohydrate Binding Module Family 28

2014-05-14T09:07:42Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM28.html
|}
</div>


== Ligand specificities ==
This module was firstly classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. Currently known CBM28s are solely from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or β-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.

== Structural Features ==
[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. Ca2+ ions in CBM28 and CBM17 are shown as green spheres in the ribbon representations (upper). Important residues in the cleft are colored yellow (aromatic), red (acidic), blue (basic), and green (neutral) on the molecular surfaces (lower). |frame|right]]

* '''Fold:''' CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the β-sandwich fold. A Ca2+ ion is bound on the back side of molecule. The Ca2+ ion is not involved in ligand binding but appears to play a structural stabilization role.
* '''Type:''' CBM28s are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
* '''Features of ligand binding:''' '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on a face (side) of the β-sandwich fold, not on an apex/edge ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

== Functionalities ==
* '''Functional role of CBM:''' CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
* '''Most Common Associated Modules:''' Endo-β-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.
* '''Binding affinities:''' As a typical endo-type (Type B) CBM, CBM28s show the Ka values of 0.7-5.2 ×104 M-1 for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high-affinity (Ka = 9.9 ×105 M-1) and low-affinity (Ka = 2.1 ×104 M-1) cites <cite>Boraston2003</cite>.

* '''Novel Applications:''' ''Bsp''CBM28 was used as the most amorphous-specific CBM in a study of photoactivated localization microscopy (PALM) <cite>Fox2013</cite>.

== Family Firsts ==
;First Identified
The first identified member is the C-terminal module in Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>

;First Structural Characterization
Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in a ligand-free form ([{{PDBlink}}1uww 1uww]) <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) ([{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite>.

== References ==
<biblio>
#Boraston2002 pmid=11743880
#Boraston2003 pmid=12427734
#Tsukimoto2010 pmid=20159017
#Notenboom2011 pmid=11733998
#Boraston2002-2 pmid=12079353
#Araki2009 pmid=19420681

#Fox2013 pmid=23563526
#Mosbah2002 pmid=12153043
#Jamal2004 pmid=15136030
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM028]]

Carbohydrate Binding Module Family 28

2014-05-14T09:05:31Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM28.html
|}
</div>


== Ligand specificities ==
This module was firstly classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. Currently known CBM28s are solely from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or β-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.

== Structural Features ==
[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. Ca2+ ions in CBM28 and CBM17 are shown as green spheres. |frame|right]]

* '''Fold:''' CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the β-sandwich fold. A Ca2+ ion is bound on the back side of molecule. The Ca2+ ion is not involved in ligand binding but appears to play a structural stabilization role.
* '''Type:''' CBM28s are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
* '''Features of ligand binding:''' '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on a face (side) of the β-sandwich fold, not on an apex/edge ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

== Functionalities ==
* '''Functional role of CBM:''' CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
* '''Most Common Associated Modules:''' Endo-β-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.
* '''Binding affinities:''' As a typical endo-type (Type B) CBM, CBM28s show the Ka values of 0.7-5.2 ×104 M-1 for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high-affinity (Ka = 9.9 ×105 M-1) and low-affinity (Ka = 2.1 ×104 M-1) cites <cite>Boraston2003</cite>.

* '''Novel Applications:''' ''Bsp''CBM28 was used as the most amorphous-specific CBM in a study of photoactivated localization microscopy (PALM) <cite>Fox2013</cite>.

== Family Firsts ==
;First Identified
The first identified member is the C-terminal module in Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>

;First Structural Characterization
Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in a ligand-free form ([{{PDBlink}}1uww 1uww]) <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) ([{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite>.

== References ==
<biblio>
#Boraston2002 pmid=11743880
#Boraston2003 pmid=12427734
#Tsukimoto2010 pmid=20159017
#Notenboom2011 pmid=11733998
#Boraston2002-2 pmid=12079353
#Araki2009 pmid=19420681

#Fox2013 pmid=23563526
#Mosbah2002 pmid=12153043
#Jamal2004 pmid=15136030
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM028]]

Carbohydrate Binding Module Family 28

2014-05-14T08:57:11Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM28.html
|}
</div>


== Ligand specificities ==
This module was firstly classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. Currently known CBM28s are solely from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or β-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.

== Structural Features ==
[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. |frame|right]]

* '''Fold:''' CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the β-sandwich fold.
* '''Type:''' CBM28s are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
* '''Features of ligand binding:''' '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on a face (side) of the β-sandwich fold, not on an apex/edge ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

== Functionalities ==
* '''Functional role of CBM:''' CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
* '''Most Common Associated Modules:''' Endo-β-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.
* '''Binding affinities:''' As a typical endo-type (Type B) CBM, CBM28s show the Ka values of 0.7-5.2 ×104 M-1 for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high-affinity (Ka = 9.9 ×105 M-1) and low-affinity (Ka = 2.1 ×104 M-1) cites <cite>Boraston2003</cite>.

* '''Novel Applications:''' ''Bsp''CBM28 was used as the most amorphous-specific CBM in a study of photoactivated localization microscopy (PALM) <cite>Fox2013</cite>.

== Family Firsts ==
;First Identified
The first identified member is the C-terminal module in Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>

;First Structural Characterization
Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in a ligand-free form ([{{PDBlink}}1uww 1uww]) <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) ([{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite>.

== References ==
<biblio>
#Boraston2002 pmid=11743880
#Boraston2003 pmid=12427734
#Tsukimoto2010 pmid=20159017
#Notenboom2011 pmid=11733998
#Boraston2002-2 pmid=12079353
#Araki2009 pmid=19420681

#Fox2013 pmid=23563526
#Mosbah2002 pmid=12153043
#Jamal2004 pmid=15136030
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM028]]

Carbohydrate Binding Module Family 42

2014-05-14T08:36:13Z

Shinya Fushinobu: /* Structural Features */

{{CuratorApproved}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM42.html
|}
</div>


== Ligand specificities ==
This module was originally identified as a non-catalytic xylan-binding domain in [[GH54]] α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51453 ''Trichoderma reesei''] PC-3-7 <cite>Nogawa1999</cite>. In 2004, it was found to be a CBM specific for an L-arabinofuranosyl group because L-arabinofuranose molecules were bound to a non-catalytic domain of [[GH54]] α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>. CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues, which are present in plant polysaccharides (hemicelluloses) such as arabinoxylan, arabinan, and arabinogalactan. Most of CBM42s are associated with α-L-arabinofuranosidases from fungi ([[GH54]]) or bacteria ([[GH43]]).

== Structural Features ==
[[Image:CBM42.png|'''Figure 1:''' CBM42 of α-L-arabinofuranosidase B from ''A. kawachii'' in complex with α-L-arabinofuranosyl-α-1,2-xylobiose (2D44). The α-domain is non-functional. |frame|right]]

* '''Fold:''' CBM42s have a β-trefoil fold that is similar to [[CBM13]] and R(ricin)-type lectins ('''Figure 1'''). The module has a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one of the three subdomains sometimes loses its function due to mutations at critical residues for ligand binding.
* '''Type:''' CBM42s are typical [[Carbohydrate-binding_modules|Type C CBMs]] that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans <cite>Miyanaga2006</cite>.
* '''Features of ligand binding:''' The binding sites are located at side pockets of the triangular structure of the β-trefoil fold. Residues important for the binding to a non-reducing end L-arabinofuranosyl group are as follows: an aspartate forming hydrogen bonds to the O2 and O3 hydroxyls, a histidine forming a hydrogen bond to the O5 hydroxyl, and two aromatic residues (tyrosine, tryptophan, or phenylalanine) stacking to the furanose sugar ('''Figure 1'''). They are D425, H416, Y417 and Y456 in the β-subdomain of AkAbfB and are conserved in functional CBM42 subdomains.
* '''Available structures:''' Several crystal structures including complex structures with compounds containing an L-arabinofuranosyl group are available. For example, AkAbfB (α-subdomain is non-functional) ([{{PDBlink}}1wd3 1wd3] [{{PDBlink}}1wd4 1wd4]) <cite>Miyanaga2004</cite>, ([{{PDBlink}}2d43 2d43] [{{PDBlink}}2d44 2d44]) <cite>Miyanaga2006</cite>; Exo-1,5-α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33903 ''Sreptomyces avermitilis''] (all subdomains are functional)([{{PDBlink}}3akf 3akf] [{{PDBlink}}3akg 3akg] [{{PDBlink}}3akh 3akh] [{{PDBlink}}3aki 3aki]) <cite>Fujimoto2010</cite>; CBM42A in Cthe_0015 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1515 ''Clostridium thermocellum''] (β-subdomain is non-functional) ([{{PDBlink}}3kmv 3kmv]) <cite>Ribeiro2010</cite>.

== Functionalities ==
* '''Functional role of CBM:''' CBM42s are thought to target catalytic modules (usually α-L-arabinofuranosidases) to hemicelluloses that have L-arabinofuranosyl termini or branches. Mutations at the binding sites of CBM42 significantly reduced the catalytic activity toward natural polysaccharides in these enzymes, whereas the activity toward ''p''-nitrophenyl α-L-arabinofuranoside was not affected <cite>Miyanaga2006 Ribeiro2010</cite>.
* '''Most Common Associated Modules:''' α-L-Arabinofuranosidases or exo-arabinanases of [[GH2]], [[GH43]], [[GH54]], [[GH93]], or non-classified GHs <cite>Ribeiro2010</cite>. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM42s are also associated with [[GH16]] or [[GH30]].
* '''Binding affinities:''' As a typical exo-type (Type C) CBM, the CBM42 in AkAbfB shows relatively low binding affinities to L-arabinofuranose-containing oligosaccharides with Ka values of 1~5 ×103 M-1. <cite>Miyanaga2006</cite>.
* '''Novel Applications:''' A CBM42 was used to create a chimeric enzyme with a feruloyl esterase <cite>Koseki2010</cite>.

== Family Firsts ==
;First Identified
The L-arabinofuranose-binding function of CBM42 was first suggested by crystallography of α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>.
;First Structural Characterization
The first structure of CBM42 was revealed in 2004 in the x-ray crystal structure of AkAbfB in complex with arabinose as a full-length structure with a catalytic [[GH54]] domain [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>.

== References ==
<biblio>
#Nogawa1999 pmid=10473402
#Miyanaga2004 pmid=15292273
#Miyanaga2006 pmid=16846393
#Fujimoto2010 pmid=20739278
#Ribeiro2010 pmid=20637315
#Koseki2010 pmid=19756576

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM042]]

Carbohydrate Binding Module Family 28

2014-05-14T08:34:59Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM28.html
|}
</div>


== Ligand specificities ==
This module was firstly classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. Currently known CBM28s are solely from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or β-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.

== Structural Features ==
[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-D (+E) from the non-reducing end to the reducing end. |frame|right]]

* '''Fold:''' CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the β-sandwich fold.
* '''Type:''' CBM28s are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
* '''Features of ligand binding:''' '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on a face (side) of the β-sandwich fold, not on an apex/edge ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

== Functionalities ==
* '''Functional role of CBM:''' CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
* '''Most Common Associated Modules:''' Endo-β-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.
* '''Binding affinities:''' As a typical endo-type (Type B) CBM, CBM28s show the Ka values of 0.7-5.2 ×104 M-1 for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high-affinity (Ka = 9.9 ×105 M-1) and low-affinity (Ka = 2.1 ×104 M-1) cites <cite>Boraston2003</cite>.

* '''Novel Applications:''' ''Bsp''CBM28 was used as the most amorphous-specific CBM in a study of photoactivated localization microscopy (PALM) <cite>Fox2013</cite>.

== Family Firsts ==
;First Identified
The first identified member is the C-terminal module in Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>

;First Structural Characterization
Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in a ligand-free form ([{{PDBlink}}1uww 1uww]) <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) ([{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite>.

== References ==
<biblio>
#Boraston2002 pmid=11743880
#Boraston2003 pmid=12427734
#Tsukimoto2010 pmid=20159017
#Notenboom2011 pmid=11733998
#Boraston2002-2 pmid=12079353
#Araki2009 pmid=19420681

#Fox2013 pmid=23563526
#Mosbah2002 pmid=12153043
#Jamal2004 pmid=15136030
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM028]]

Carbohydrate Binding Module Family 28

2014-05-14T08:18:41Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM28.html
|}
</div>


== Ligand specificities ==
This module was firstly classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. Currently known CBM28s are solely from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or β-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.

== Structural Features ==
[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-D (+E) from the non-reducing end to the reducing end. |frame|right]]

* '''Fold:''' CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the β-sandwich fold.
* '''Type:''' CBM28s are typical endo-type [[Carbohydrate-binding_modules|Type C CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
* '''Features of ligand binding:''' '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on a face (side) of the β-sandwich fold ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

== Functionalities ==
* '''Functional role of CBM:''' CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
* '''Most Common Associated Modules:''' Endo-β-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.
* '''Binding affinities:''' As a typical endo-type (Type B) CBM, CBM28s show the Ka values of 0.7-5.2 ×104 M-1 for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high- (Ka = 9.9 ×105 M-1) and low-affinity (Ka = 2.1 ×104 M-1) cites <cite>Boraston2003</cite>.

* '''Novel Applications:''' ''Bsp''CBM28 was used as a most amorphous-specific CBM in a study of photo activated localization microscopy (PALM) <cite>Fox2013</cite>.

== Family Firsts ==
;First Identified
The first identified member is the C-terminal module in Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>

;First Structural Characterization
Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in a ligand-free form [{{PDBlink}}1uww 1uww] <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) [{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci].

== References ==
<biblio>
#Boraston2002 pmid=11743880
#Boraston2003 pmid=12427734
#Tsukimoto2010 pmid=20159017
#Notenboom2011 pmid=11733998
#Boraston2002-2 pmid=12079353
#Araki2009 pmid=19420681

#Fox2013 pmid=23563526
#Mosbah2002 pmid=12153043
#Jamal2004 pmid=15136030
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM028]]

Carbohydrate Binding Module Family 28

2014-05-14T07:42:10Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM28.html
|}
</div>


== Ligand specificities ==
This module was firstly classified in 2002 by a study of the C-terminal module in [[CH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. Currently known CBM28s are solely from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or β-1,3-1,4-glucans <cite>Boraston2003</cite>.

== Structural Features ==
[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-D (+E) from the non-reducing end to the reducing end. |frame|right]]

* '''Fold:''' CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the β-sandwich fold.
* '''Type:''' CBM28s are typical endo-type [[Carbohydrate-binding_modules|Type C CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
* '''Features of ligand binding:''' '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on a face (side) of the β-sandwich fold ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

== Functionalities ==
* '''Functional role of CBM:''' CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
* '''Most Common Associated Modules:''' Endo-β-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.
* '''Novel Applications:''' ''Bsp''CBM28 was used as a most amorphous-specific CBM in a study of photo activated localization microscopy (PALM) <cite>Fox2013</cite>.

== Family Firsts ==
;First Identified
The first identified member is the C-terminal module in Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>

;First Structural Characterization
Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in a ligand-free form [{{PDBlink}}1uww 1uww] <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) [{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci].

== References ==
<biblio>
#Boraston2002 pmid=11743880
#Boraston2003 pmid=12427734
#Tsukimoto2010 pmid=20159017

#Notenboom2011 pmid=11733998

#Boraston2002-2 pmid=12079353

#Fox2013 pmid=23563526
#Mosbah2002 pmid=12153043
#Jamal2004 pmid=15136030

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM028]]

File:CBM28-17-4.png

2014-05-14T04:14:59Z

Shinya Fushinobu: CBM28 in comparison with CBM17 and CBM4

CBM28 in comparison with CBM17 and CBM4

Carbohydrate Binding Module Family 42

2014-05-14T03:45:49Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM42.html
|}
</div>


== Ligand specificities ==
This module was originally identified as a non-catalytic xylan-binding domain in [[GH54]] α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51453 ''Trichoderma reesei''] PC-3-7 <cite>Nogawa1999</cite>. In 2004, it was found to be a CBM specific for an L-arabinofuranosyl group because L-arabinofuranose molecules were bound to a non-catalytic domain of [[GH54]] α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>. CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues, which are present in plant polysaccharides (hemicelluloses) such as arabinoxylan, arabinan, and arabinogalactan. Most of CBM42s are associated with α-L-arabinofuranosidases from fungi ([[GH54]]) or bacteria ([[GH43]]).

== Structural Features ==
[[Image:CBM42.png|'''Figure 1:''' CBM42 of α-L-arabinofuranosidase B from ''A. kawachii'' in complex with α-L-arabinofuranosyl-α-1,2-xylobiose (2D44). The α-domain is non-functional. |frame|right]]

* '''Fold:''' CBM42s have a β-trefoil fold that is similar to [[CBM13]] and R(ricin)-type lectins ('''Figure 1'''). The module has a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one of the three subdomains sometimes loses its function due to mutations at critical residues for ligand binding.
* '''Type:''' CBM42s are typical [[Carbohydrate-binding_modules|Type C CBMs]] that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans <cite>Miyanaga2006</cite>.
* '''Features of ligand binding:''' The binding sites are located at side pockets of the triangular structure of the β-trefoil fold. Residues important for the binding to a non-reducing end L-arabinofuranosyl group are as follows: an aspartate forming hydrogen bonds to the O2 and O3 hydroxyls, a histidine forming a hydrogen bond to the O5 hydroxyl, and two aromatic residues (tyrosine, tryptophan, or phenylalanine) stacking to the furanose sugar ('''Figure 1'''). They are D425, H416, Y417 and Y456 in the β-subdomain of AkAbfB and are conserved in functional CBM42 subdomains.
* '''Available structures:''' Several crystal structures including complex structures with compounds containing an L-arabinofuranosyl group are available. For example, AkAbfB (α-subdomain is non-functional) [{{PDBlink}}1wd3 1wd3] [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>, [{{PDBlink}}2d43 2d43] [{{PDBlink}}2d44 2d44] <cite>Miyanaga2006</cite>; Exo-1,5-α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33903 ''Sreptomyces avermitilis''] (all subdomains are functional)[{{PDBlink}}3akf 3akf] [{{PDBlink}}3akg 3akg] [{{PDBlink}}3akh 3akh] [{{PDBlink}}3aki 3aki] <cite>Fujimoto2010</cite>; CBM42A in Cthe_0015 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1515 ''Clostridium thermocellum''] (β-subdomain is non-functional) [{{PDBlink}}3KMV 3KMV] <cite>Ribeiro2010</cite>.

== Functionalities ==
* '''Functional role of CBM:''' CBM42s are thought to target catalytic modules (usually α-L-arabinofuranosidases) to hemicelluloses that have L-arabinofuranosyl termini or branches. Mutations at the binding sites of CBM42 significantly reduced the catalytic activity toward natural polysaccharides in these enzymes, whereas the activity toward ''p''-nitrophenyl α-L-arabinofuranoside was not affected <cite>Miyanaga2006 Ribeiro2010</cite>.
* '''Most Common Associated Modules:''' α-L-Arabinofuranosidases or exo-arabinanases of [[GH2]], [[GH43]], [[GH54]], [[GH93]], or non-classified GHs <cite>Ribeiro2010</cite>. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM42s are also associated with [[GH16]] or [[GH30]].
* '''Binding affinities:''' As a typical exo-type (Type C) CBM, the CBM42 in AkAbfB shows relatively low binding affinities to L-arabinofuranose-containing oligosaccharides with Ka values of 1~5 ×103 M-1. <cite>Miyanaga2006</cite>.
* '''Novel Applications:''' A CBM42 was used to create a chimeric enzyme with a feruloyl esterase <cite>Koseki2010</cite>.

== Family Firsts ==
;First Identified
The L-arabinofuranose-binding function of CBM42 was first suggested by crystallography of α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>.
;First Structural Characterization
The first structure of CBM42 was revealed in 2004 in the x-ray crystal structure of AkAbfB in complex with arabinose as a full-length structure with a catalytic [[GH54]] domain [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>.

== References ==
<biblio>
#Nogawa1999 pmid=10473402
#Miyanaga2004 pmid=15292273
#Miyanaga2006 pmid=16846393
#Fujimoto2010 pmid=20739278
#Ribeiro2010 pmid=20637315
#Koseki2010 pmid=19756576

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM042]]

User:Shinya Fushinobu

2014-05-13T13:49:44Z

Shinya Fushinobu:

[[Image:Fushinobu.jpg|200px|right]]

I am a Professor at [http://enzyme13.bt.a.u-tokyo.ac.jp/index-e.html Laboratory of Enzymology] in Department of Biotechnology, [http://www.a.u-tokyo.ac.jp/english/index.html Graduate School of Agricultural and Life Sciences], [http://www.u-tokyo.ac.jp/index_e.html The University of Tokyo] located in Tokyo, Japan. Raised in [http://www.city.kure.hiroshima.jp/english/index.html Kure], Hiroshima, Japan. I obtained Ph.D degree in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern structure and function of enzymes, mainly those of Carbohydrate-Active enZymes. My home page is [http://enzyme13.bt.a.u-tokyo.ac.jp/fushi/index-e.html here]. I contributed to three-dimensional structure determination of

*[[GH1]] ''Phanerochaete chrysosporium'' β-glucosidase 1B (BGL1B) <cite>Nijikken2007</cite>
*[[GH3]] ''Kluyveromyces marxianus'' β-glucosidase (''Km''BglI) <cite>Yoshida2010</cite>
*[[GH3]] ''Aspergillus aculeatus'' β-glucosidase (''Aa''BGL1) <cite>Suzuki2013</cite>
*[[GH8]] ''Bacillus halodurans'' reducing-end xylose-releasing exo-oligoxylanase (Rex) <cite>Fushinobu2005</cite>
*[[GH10]] ''Clostridium stercorarium'' xylanase B (XynB) <cite>Nishimoto2007</cite>
*[[GH11]] ''Aspergillus kawachii'' xylanase C (XynC) <cite>Fushinobu1998</cite>
*[[GH20]] ''Bifidobacterium bifidum'' lacto-''N''-biosidase (''Bb''LNBase) <cite>Ito2013</cite>
*[[GH26]] β-mannanase from a symbiotic protist of the termite ''Reticulitermes speratus'' (''Rs''Man26C) <cite>Tsukagoshi2014</cite>
*[[GH29]] ''Bifidobacterium longum'' subsp. ''infantis'' 1,3-1,4-α-L-fucosidase (''Bi''AfcB) <cite>Sakurama2012</cite>
*[[GH42]] ''Thermus thermophilus'' β-galactosidase (A4-β-Gal) '''Family First''' <cite>Hidaka2002</cite>
*[[GH51]] ''Thermotoga maritima'' α-L-arabinofuranosidase (''Tm''-AFase) <cite>Im2012</cite>
*[[GH54]] ''Aspergillus kawachii'' α-L-arabinofuranosidase B (AkAbfB) '''Family First''' plus identification of [[CBM42]] <cite>Miyanaga2004</cite>
*[[GH55]] ''Phanerochaete chrysosporium'' β-1,3-glucanase (Lam55A) '''Family First''' <cite>Ishida2009</cite>
*[[GH57]] ''Thermococcus litoralis'' 4-α-glucanotransferase (TLGT) '''Family First''' <cite>Imamura2003</cite>
*[[GH65]] ''Caldicellulosiruptor saccharolyticus'' kojibiose phosphorylase (CsKP) <cite>Okada2013</cite>
*[[GH94]] ''Vibrio proteolyticus'' chitobiose phosphorylase (ChBP) '''Family First''' <cite>Hidaka2004</cite>
*[[GH94]] ''Cellvibrio gilvus'' cellobiose phosphorylase (CBP) <cite>Hidaka2006</cite>
*[[GH101]] ''Bifidobacterium longum'' endo-α-''N''-acetylgalactosaminidase (EngBF) <cite>Suzuki2009</cite>
*[[GH112]] ''Bifidobacterium longum'' galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) '''Family First''' <cite>Hidaka2009</cite>
*[[GH127]] ''Bifidobacterium longum'' β-L-arabinofuranosidase (HypBA1) '''Family First''' <cite>Ito2014</cite>

*PL20 ''Trichoderma reesei'' endo-β-1,4-glucuronan lyase (TrGL) '''Family First''' <cite>Konno2009</cite>
*[[CBM28]] in ''Clostridium josui'' Cel5A (''Cj''CBM28) <cite>Tsukimoto2010</cite>

----

<biblio>
#Nijikken2007 pmid=17376440
#Yoshida2010 pmid=20662765
#Suzuki2013 pmid=23537284
#Fushinobu2005 pmid=15718242
#Nishimoto2007 pmid=17383976
#Fushinobu1998 pmid=9930661
#Ito2013 pmid=23479733
#Tsukagoshi2014 pmid=24570006

#Sakurama2012 pmid=22451675
#Hidaka2002 pmid=12215416

#Miyanaga2004 pmid=15292273
#Ishida2009 pmid=19193645
#Imamura2003 pmid=12618437
#Okada2013 pmid=24255995

#Hidaka2004 pmid=15274915

#Hidaka2006 pmid=16646954
#Suzuki2009 pmid=19502354
#Hidaka2009 pmid=19124470
#Konno2009 pmid=19306878
#Tsukimoto2010 pmid=20159017
#Im2012 pmid=22313787

#Ito2014 pmid=24680821

</biblio>

[[Category:Contributors|Fushinobu, Shinya]]

Carbohydrate Binding Module Family 42

2014-05-13T13:37:55Z

Shinya Fushinobu:

{{CuratorApproved}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM42.html
|}
</div>


== Ligand specificities ==
This module was originally identified as a non-catalytic xylan-binding domain in [[GH54]] α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51453 ''Trichoderma reesei''] PC-3-7 <cite>Nogawa1999</cite>. In 2004, it was found to be a CBM specific for an L-arabinofuranosyl group because L-arabinofuranose molecules were bound to a non-catalytic domain of [[GH54]] α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>. CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues, which are present in plant polysaccharides (hemicelluloses) such as arabinoxylan, arabinan, and arabinogalactan. Most of CBM42s are associated with α-L-arabinofuranosidases from fungi ([[GH54]]) or bacteria ([[GH43]]).

== Structural Features ==
[[Image:CBM42.png|'''Figure 1:''' CBM42 of α-L-arabinofuranosidase B from ''A. kawachii'' in complex with α-L-arabinofuranosyl-α-1,2-xylobiose (2D44). The α-domain is non-functional. |frame|right]]

* '''Fold:''' CBM42s have a β-trefoil fold that is similar to [[CBM13]] and R(ricin)-type lectins ('''Figure 1'''). The module has a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one of the three subdomains sometimes loses its function due to mutations at critical residues for ligand binding.
* '''Type:''' CBM42s are typical [[Carbohydrate-binding_modules|Type C CBMs]] that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans <cite>Miyanaga2006</cite>.
* '''Features of ligand binding:''' The binding sites are located at side pockets of the triangular structure of the β-trefoil fold. Residues important for the binding to a non-reducing end L-arabinofuranosyl group are as follows: an aspartate forming hydrogen bonds to the O2 and O3 hydroxyls, a histidine forming a hydrogen bond to the O5 hydroxyl, and two aromatic residues (tyrosine, tryptophan, or phenylalanine) stacking to the furanose sugar ('''Figure 1'''). They are D425, H416, Y417 and Y456 in the β-subdomain of AkAbfB and are conserved in functional CBM42 subdomains.
* '''Available structures:''' Several crystal structures including complex structures with compounds containing an L-arabinofuranosyl group are available. For example, AkAbfB (α-subdomain is non-functional) [{{PDBlink}}1wd3 1wd3] [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>, [{{PDBlink}}2d43 2d43] [{{PDBlink}}2d44 2d44] <cite>Miyanaga2006</cite>; Exo-1,5-α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33903 ''Sreptomyces avermitilis''] (all subdomains are functional)[{{PDBlink}}3akf 3akf] [{{PDBlink}}3akg 3akg] [{{PDBlink}}3akh 3akh] [{{PDBlink}}3aki 3aki] <cite>Fujimoto2010</cite>; CBM42A in Cthe_0015 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1515 ''Clostridium thermocellum''] (β-subdomain is non-functional) [{{PDBlink}}3KMV 3KMV] <cite>Ribeiro2010</cite>.

== Functionalities ==
* '''Functional role of CBM:''' CBM42s are thought to target catalytic modules (usually α-L-arabinofuranosidases) to hemicelluloses that have L-arabinofuranosyl termini or branches. Mutations at the binding sites of CBM42 significantly reduced the catalytic activity toward natural polysaccharides in these enzymes, whereas the activity toward ''p''-nitrophenyl α-L-arabinofuranoside was not affected <cite>Miyanaga2006 Ribeiro2010</cite>.
* '''Most Common Associated Modules:''' α-L-Arabinofuranosidases or exo-arabinanases of [[GH2]], [[GH43]], [[GH54]], [[GH93]], or non-classified GHs <cite>Ribeiro2010</cite>. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM42s are also associated with [[GH16]] or [[GH30]].
* '''Novel Applications:''' A CBM42 was used to create a chimeric enzyme with a feruloyl esterase <cite>Koseki2010</cite>.

== Family Firsts ==
;First Identified
The L-arabinofuranose-binding function of CBM42 was first suggested by crystallography of α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>.
;First Structural Characterization
The first structure of CBM42 was revealed in 2004 in the x-ray crystal structure of AkAbfB in complex with arabinose as a full-length structure with a catalytic [[GH54]] domain [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>.

== References ==
<biblio>
#Nogawa1999 pmid=10473402
#Miyanaga2004 pmid=15292273
#Miyanaga2006 pmid=16846393
#Fujimoto2010 pmid=20739278
#Ribeiro2010 pmid=20637315
#Koseki2010 pmid=19756576

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM042]]

User:Shinya Fushinobu

2014-05-13T12:31:22Z

Shinya Fushinobu:

[[Image:Fushinobu.jpg|200px|right]]

I am a Professor at [http://enzyme13.bt.a.u-tokyo.ac.jp/index-e.html Laboratory of Enzymology] in Department of Biotechnology, [http://www.a.u-tokyo.ac.jp/english/index.html Graduate School of Agricultural and Life Sciences], [http://www.u-tokyo.ac.jp/index_e.html The University of Tokyo] located in Tokyo, Japan. Raised in [http://www.city.kure.hiroshima.jp/english/index.html Kure], Hiroshima, Japan. I obtained Ph.D degree in Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern structure and function of enzymes, mainly those of Carbohydrate-Active enZymes. My home page is [http://enzyme13.bt.a.u-tokyo.ac.jp/fushi/index-e.html here]. I contributed to three-dimensional structure determination of

*[[GH1]] ''Phanerochaete chrysosporium'' β-glucosidase 1B (BGL1B) <cite>Nijikken2007</cite>
*[[GH3]] ''Kluyveromyces marxianus'' β-glucosidase (''Km''BglI) <cite>Yoshida2010</cite>
*[[GH3]] ''Aspergillus aculeatus'' β-glucosidase (''Aa''BGL1) <cite>Suzuki2013</cite>
*[[GH8]] ''Bacillus halodurans'' reducing-end xylose-releasing exo-oligoxylanase (Rex) <cite>Fushinobu2005</cite>
*[[GH10]] ''Clostridium stercorarium'' xylanase B (XynB) <cite>Nishimoto2007</cite>
*[[GH11]] ''Aspergillus kawachii'' xylanase C (XynC) <cite>Fushinobu1998</cite>
*[[GH20]] ''Bifidobacterium bifidum'' lacto-''N''-biosidase (''Bb''LNBase) <cite>Ito2013</cite>
*[[GH29]] ''Bifidobacterium longum'' subsp. ''infantis'' 1,3-1,4-α-L-fucosidase (''Bi''AfcB) <cite>Sakurama2012</cite>
*[[GH42]] ''Thermus thermophilus'' β-galactosidase (A4-β-Gal) '''Family First''' <cite>Hidaka2002</cite>
*[[GH51]] ''Thermotoga maritima'' α-L-arabinofuranosidase (''Tm''-AFase) <cite>Im2012</cite>
*[[GH54]] ''Aspergillus kawachii'' α-L-arabinofuranosidase B (AkAbfB) '''Family First''' plus identification of [[CBM42]] <cite>Miyanaga2004</cite>
*[[GH55]] ''Phanerochaete chrysosporium'' β-1,3-glucanase (Lam55A) '''Family First''' <cite>Ishida2009</cite>
*[[GH57]] ''Thermococcus litoralis'' 4-α-glucanotransferase (TLGT) '''Family First''' <cite>Imamura2003</cite>
*[[GH94]] ''Vibrio proteolyticus'' chitobiose phosphorylase (ChBP) '''Family First''' <cite>Hidaka2004</cite>
*[[GH94]] ''Cellvibrio gilvus'' cellobiose phosphorylase (CBP) <cite>Hidaka2006</cite>
*[[GH101]] ''Bifidobacterium longum'' endo-α-''N''-acetylgalactosaminidase (EngBF) <cite>Suzuki2009</cite>
*[[GH112]] ''Bifidobacterium longum'' galacto-''N''-biose/lacto-''N''-biose I phosphorylase (GLNBP) '''Family First''' <cite>Hidaka2009</cite>
*PL20 ''Trichoderma reesei'' endo-β-1,4-glucuronan lyase (TrGL) '''Family First''' <cite>Konno2009</cite>
*[[CBM28]] in ''Clostridium josui'' Cel5A (''Cj''CBM28) <cite>Tsukimoto2010</cite>

----

<biblio>
#Nijikken2007 pmid=17376440
#Yoshida2010 pmid=20662765
#Suzuki2013 pmid=23537284
#Fushinobu2005 pmid=15718242
#Nishimoto2007 pmid=17383976
#Fushinobu1998 pmid=9930661
#Ito2013 pmid=23479733
#Hidaka2002 pmid=12215416
#Miyanaga2004 pmid=15292273
#Ishida2009 pmid=19193645
#Imamura2003 pmid=12618437
#Hidaka2004 pmid=15274915
#Hidaka2006 pmid=16646954
#Suzuki2009 pmid=19502354
#Hidaka2009 pmid=19124470
#Konno2009 pmid=19306878
#Tsukimoto2010 pmid=20159017
#Im2012 pmid=22313787
#Sakurama2012 pmid=22451675
</biblio>

[[Category:Contributors|Fushinobu, Shinya]]

Carbohydrate Binding Module Family 42

2014-05-13T11:54:09Z

Shinya Fushinobu:

{{UnderConstruction}}
* [[Author]]: ^^^Shinya Fushinobu^^^
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM42.html
|}
</div>


== Ligand specificities ==
This module was originally identified as a non-catalytic xylan-binding domain in [[GH54]] α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=51453 ''Trichoderma reesei''] PC-3-7 <cite>Nogawa1999</cite>. In 2004, it was found to be a CBM specific for an L-arabinofuranosyl group because L-arabinofuranose molecules were bound to a non-catalytic domain of [[GH54]] α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>. CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues, which are present in plant polysaccharides (hemicelluloses) such as arabinoxylan, arabinan, and arabinogalactan. Most of CBM42s are associated with α-L-arabinofuranosidases from fungi ([[GH54]]) or bacteria ([[GH43]]).

== Structural Features ==
[[Image:CBM42.png|'''Figure 1:''' CBM42 of α-L-arabinofuranosidase B from ''A. kawachii'' in complex with α-L-arabinofuranosyl-α-1,2-xylobiose (2D44). The α-domain is non-functional. |frame|right]]

* '''Fold:''' CBM42s have a β-trefoil fold that is similar to [[CBM13]] and R(ricin)-type lectins ('''Figure 1'''). The module has a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one of the three subdomains sometimes loses its function due to mutations at critical residues for ligand binding.
* '''Type:''' CBM42s are typical [[Carbohydrate-binding_modules|Type C CBMs]] that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans <cite>Miyanaga2006</cite>.
* '''Features of ligand binding:''' The binding sites are located at side pockets of the triangular structure of the β-trefoil fold. Residues important for the binding to a non-reducing end L-arabinofuranosyl group are as follows: an aspartate forming hydrogen bonds to the O2 and O3 hydroxyls, a histidine forming a hydrogen bond to the O5 hydroxyl, and two aromatic residues (tyrosine, tryptophan, or phenylalanine) stacking to the furanose sugar ('''Figure 1'''). They are D425, H416, Y417 and Y456 in the β-subdomain of AkAbfB and are conserved in functional CBM42 subdomains.
* '''Available structures:''' Several crystal structures including complex structures with compounds containing an L-arabinofuranosyl group are available. For example, AkAbfB (α-subdomain is non-functional) [{{PDBlink}}1wd3 1wd3] [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>, [{{PDBlink}}2d43 2d43] [{{PDBlink}}2d44 2d44] <cite>Miyanaga2006</cite>; Exo-1,5-α-L-arabinofuranosidase from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33903 ''Sreptomyces avermitilis''] (all subdomains are functional)[{{PDBlink}}3akf 3akf] [{{PDBlink}}3akg 3akg] [{{PDBlink}}3akh 3akh] [{{PDBlink}}3aki 3aki] <cite>Fujimoto2010</cite>; CBM42A in Cthe_0015 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1515 ''Clostridium thermocellum''] (β-subdomain is non-functional) [{{PDBlink}}3KMV 3KMV] <cite>Ribeiro2010</cite>.

== Functionalities ==
* '''Functional role of CBM:''' CBM42s are thought to target catalytic modules (usually α-L-arabinofuranosidases) to hemicelluloses that have L-arabinofuranosyl termini or branches. Mutations at the binding sites of CBM42 significantly reduced the catalytic activity toward natural polysaccharides in these enzymes, whereas the activity toward ''p''-nitrophenyl α-L-arabinofuranoside was not affected <cite>Miyanaga2006 Ribeiro2010</cite>.
* '''Most Common Associated Modules:''' α-L-Arabinofuranosidases or exo-arabinanases of [[GH2]], [[GH43]], [[GH54]], [[GH93]], or non-classified GHs <cite>Ribeiro2010</cite>. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM42s are also associated with [[GH16]] or [[GH30]].
* '''Novel Applications:''' A CBM42 was used to create a chimeric enzyme with a feruloyl esterase <cite>Koseki2010</cite>.

== Family Firsts ==
;First Identified
The L-arabinofuranose-binding function of CBM42 was first suggested by crystallography of α-L-arabinofuranosidase B from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40384 ''Aspergillus kawachii''] (AkAbfB) <cite>Miyanaga2004</cite>.
;First Structural Characterization
The first structure of CBM42 was revealed in 2004 in the x-ray crystal structure of AkAbfB in complex with arabinose as a full-length structure with a catalytic [[GH54]] domain [{{PDBlink}}1wd4 1wd4] <cite>Miyanaga2004</cite>.

== References ==
<biblio>
#Nogawa1999 pmid=10473402
#Miyanaga2004 pmid=15292273
#Miyanaga2006 pmid=16846393
#Fujimoto2010 pmid=20739278
#Ribeiro2010 pmid=20637315
#Koseki2010 pmid=19756576

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM042]]