Glycoside Hydrolase Family 74 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:19:20Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Harry Brumer at 22:35, 25 September 2019

2019-09-25T22:35:41Z

Harry Brumer at 22:29, 25 September 2019

2019-09-25T22:29:09Z

Takuya Ishida at 23:39, 14 May 2011

2011-05-14T23:39:54Z

Takuya Ishida at 11:15, 14 May 2011

2011-05-14T11:15:28Z

Takuya Ishida at 14:59, 13 May 2011

2011-05-13T14:59:04Z

Spencer Williams at 11:25, 12 May 2011

2011-05-12T11:25:54Z

Harry Brumer: fixed Yaoi2004 reference issues

2011-05-09T07:37:21Z

fixed Yaoi2004 reference issues

Katsuro Yaoi at 04:17, 9 May 2011

2011-05-09T04:17:37Z

Katsuro Yaoi at 02:23, 9 May 2011

2011-05-09T02:23:09Z

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Katsuro Yaoi^^^ and ^^^Takuya Ishida^^^
+* [[Author]]: [[User:Katsuro Yaoi|Katsuro Yaoi]] and [[User:Takuya Ishida|Takuya Ishida]]
-* [[Responsible Curator]]:  ^^^Katsuro Yaoi^^^
+* [[Responsible Curator]]:  [[User:Katsuro Yaoi|Katsuro Yaoi]]
 ----

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 == Substrate specificities ==
-[[Glycoside hydrolases]] of this family hydrolyze &beta;-1,4-linkages of various glucans. With the exception of Cel74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2336 ''Thermotoga maritima''], all biochemically characterized enzymes are specific toward xyloglucans and/or xyloglucan-oligosaccharides. Cel74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2336 ''Thermotoga maritima''] exhibits the highest activity on barley &beta;-glucan, with relative activity of 20% toward xyloglucan <cite>Chhabra2002</cite>. A wide diversity in the modes of action by GH74 enzymes has been reported. "Oligoxyloglucan reducing end-specific cellobiohydrolase (OXG-RCBH, EC [{{EClink}}3.2.1.150 3.2.1.150])" from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=203496 ''Geotrichum sp. M128''] <cite>Yaoi2002</cite> and "oligoxyloglucan reducing end-specific xyloglucanobiohydrolase (OREX)" from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=162425 ''Emericella nidulans''] (formerly known as ''Aspergillus nidulans'') <cite>Bauer2005</cite> are active on only xyloglucan oligosaccharides and have essentially no ability to degrade xyloglucan polysaccharides. They release oligosaccharides with two glucose units from non-reducing end of xyloglucan oligosaccharides. On the other hand, GH74 enzymes designated as xyloglucanase; xyloglucan specific endo-&beta;-1,4-glucanases: XEG; and xyloglucan hydrolases: Xgh, (EC [{{EClink}}3.2.1.151 3.2.1.151]), exhibit endo-type activity on xyloglucan from tamarind seed, a readily available and well-investigated xyloglucan <cite>York1993</cite>. Many GH74 xyloglucanases hydrolyze the glycosidic linkage of unbranched glucose residues, but several members including ''Geotrichum sp.'' OXG-RCBH <cite>Yaoi2002</cite>, ''E. nidulans'' OREX <cite>Bauer2005</cite>, and [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=51453''Hypocrea jecorina''] (formerly known as ''Trichoderma reesei'') Cel74A <cite>Desmet2007</cite> accommodate side-chain xylose residues at [[Sub-site nomenclature|subsite]] -1 of the active site.  As first elucidated by Matsuzawa, Saito, and Yaoi <cite>Matsuzawa2014</cite>, some GH74 members exhibit processivity (multiple catalytic events before chain dissociation) in xyloglucan hydrolysis, which is related to active-site length and the presence of key aromatic residues, and which follows protein phylogeny <cite>Arnal2019</cite>.
+[[Glycoside hydrolases]] of this family hydrolyze &beta;-1,4-linkages of various glucans. With the exception of Cel74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2336 ''Thermotoga maritima''], all biochemically characterized enzymes are specific toward xyloglucans and/or xyloglucan-oligosaccharides (reviewed in <cite>Arnal2019</cite>). Cel74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2336 ''Thermotoga maritima''] exhibits the highest activity on barley &beta;-glucan, with relative activity of 20% toward xyloglucan <cite>Chhabra2002</cite>. A wide diversity in the modes of action by GH74 enzymes has been reported. "Oligoxyloglucan reducing end-specific cellobiohydrolase (OXG-RCBH, EC [{{EClink}}3.2.1.150 3.2.1.150])" from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=203496 ''Geotrichum sp. M128''] <cite>Yaoi2002</cite> and "oligoxyloglucan reducing end-specific xyloglucanobiohydrolase (OREX)" from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=162425 ''Emericella nidulans''] (formerly known as ''Aspergillus nidulans'') <cite>Bauer2005</cite> are active on only xyloglucan oligosaccharides and have essentially no ability to degrade xyloglucan polysaccharides. They release oligosaccharides with two glucose units from non-reducing end of xyloglucan oligosaccharides. On the other hand, GH74 enzymes designated as xyloglucanase; xyloglucan specific endo-&beta;-1,4-glucanases: XEG; and xyloglucan hydrolases: Xgh, (EC [{{EClink}}3.2.1.151 3.2.1.151]), exhibit endo-type activity on xyloglucan from tamarind seed, a readily available and well-investigated xyloglucan <cite>York1993</cite>. Many GH74 xyloglucanases hydrolyze the glycosidic linkage of unbranched glucose residues, but several members including ''Geotrichum sp.'' OXG-RCBH <cite>Yaoi2002</cite>, ''E. nidulans'' OREX <cite>Bauer2005</cite>, and [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=51453''Hypocrea jecorina''] (formerly known as ''Trichoderma reesei'') Cel74A <cite>Desmet2007</cite> accommodate side-chain xylose residues at [[Sub-site nomenclature|subsite]] -1 of the active site.  As first elucidated by Matsuzawa, Saito, and Yaoi <cite>Matsuzawa2014</cite>, some GH74 members exhibit processivity (multiple catalytic events before chain dissociation) in xyloglucan hydrolysis, which is related to active-site length and the presence of key aromatic residues, and which follows protein phylogeny <cite>Arnal2019</cite>.
 == Kinetics and Mechanism ==

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of this family hydrolyze &beta;-1,4-linkages of various glucans. With the exception of Cel74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2336 ''Thermotoga maritima''], all biochemically characterized enzymes are specific toward xyloglucans and/or xyloglucan-oligosaccharides. Cel74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2336 ''Thermotoga maritima''] exhibits the highest activity on barley &beta;-glucan, with relative activity of 20% toward xyloglucan <cite>Chhabra2002</cite>. A wide diversity in the modes of action by GH74 enzymes has been reported. "Oligoxyloglucan reducing end-specific cellobiohydrolase (OXG-RCBH, EC [{{EClink}}3.2.1.150 3.2.1.150])" from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=203496 ''Geotrichum sp. M128''] <cite>Yaoi2002</cite> and "oligoxyloglucan reducing end-specific xyloglucanobiohydrolase (OREX)" from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=162425 ''Emericella nidulans''] (formerly known as ''Aspergillus nidulans'') <cite>Bauer2005</cite> are active on only xyloglucan oligosaccharides and have essentially no ability to degrade xyloglucan polysaccharides. They release oligosaccharides with two glucose units from non-reducing end of xyloglucan oligosaccharides. On the other hand, GH74 enzymes designated as xyloglucanase; xyloglucan specific endo-&beta;-1,4-glucanases: XEG; and xyloglucan hydrolases: Xgh, (EC [{{EClink}}3.2.1.151 3.2.1.151]), exhibit endo-type activity on xyloglucan from tamarind seed, a readily available and well-investigated xyloglucan <cite>York1993</cite>. Many GH74 xyloglucanases hydrolyze the glycosidic linkage of unbranched glucose residues, but several members including ''Geotrichum sp.'' OXG-RCBH <cite>Yaoi2002</cite>, ''E. nidulans'' OREX <cite>Bauer2005</cite>, and [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=51453''Hypocrea jecorina''] (formerly known as ''Trichoderma reesei'') Cel74A <cite>Desmet2007</cite> accommodate side-chain xylose residues at [[Sub-site nomenclature|subsite]] -1 of the active site.
+[[Glycoside hydrolases]] of this family hydrolyze &beta;-1,4-linkages of various glucans. With the exception of Cel74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2336 ''Thermotoga maritima''], all biochemically characterized enzymes are specific toward xyloglucans and/or xyloglucan-oligosaccharides. Cel74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2336 ''Thermotoga maritima''] exhibits the highest activity on barley &beta;-glucan, with relative activity of 20% toward xyloglucan <cite>Chhabra2002</cite>. A wide diversity in the modes of action by GH74 enzymes has been reported. "Oligoxyloglucan reducing end-specific cellobiohydrolase (OXG-RCBH, EC [{{EClink}}3.2.1.150 3.2.1.150])" from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=203496 ''Geotrichum sp. M128''] <cite>Yaoi2002</cite> and "oligoxyloglucan reducing end-specific xyloglucanobiohydrolase (OREX)" from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=162425 ''Emericella nidulans''] (formerly known as ''Aspergillus nidulans'') <cite>Bauer2005</cite> are active on only xyloglucan oligosaccharides and have essentially no ability to degrade xyloglucan polysaccharides. They release oligosaccharides with two glucose units from non-reducing end of xyloglucan oligosaccharides. On the other hand, GH74 enzymes designated as xyloglucanase; xyloglucan specific endo-&beta;-1,4-glucanases: XEG; and xyloglucan hydrolases: Xgh, (EC [{{EClink}}3.2.1.151 3.2.1.151]), exhibit endo-type activity on xyloglucan from tamarind seed, a readily available and well-investigated xyloglucan <cite>York1993</cite>. Many GH74 xyloglucanases hydrolyze the glycosidic linkage of unbranched glucose residues, but several members including ''Geotrichum sp.'' OXG-RCBH <cite>Yaoi2002</cite>, ''E. nidulans'' OREX <cite>Bauer2005</cite>, and [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=51453''Hypocrea jecorina''] (formerly known as ''Trichoderma reesei'') Cel74A <cite>Desmet2007</cite> accommodate side-chain xylose residues at [[Sub-site nomenclature|subsite]] -1 of the active site.  As first elucidated by Matsuzawa, Saito, and Yaoi <cite>Matsuzawa2014</cite>, some GH74 members exhibit processivity (multiple catalytic events before chain dissociation) in xyloglucan hydrolysis, which is related to active-site length and the presence of key aromatic residues, and which follows protein phylogeny <cite>Arnal2019</cite>.
 == Kinetics and Mechanism ==
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 == Three-dimensional structures ==
-Overall structures of GH74 enzymes consist of a tandem repeat of two seven-bladed &beta;-propeller domains. The two domains form a substrate binding cleft at the interface. The catalytic residues are located in the middle of this cleft. One side of the binding cleft of OXG-RCBH is blocked by a so-called 'exo-loop' which is found only in exo-acting enzymes in this family <cite>Yaoi2004</cite>. A crystal structure of a complex with xyloglucan-derived oligosaccharides elucidated the interaction with the side-chains of the substrate by these enzymes <cite>Martinez-Fleites2006</cite>.
+Overall structures of GH74 enzymes consist of a tandem repeat of two seven-bladed &beta;-propeller domains. The two domains form a substrate binding cleft at the interface. The catalytic residues are located in the middle of this cleft. One side of the binding cleft of OXG-RCBH is blocked by a so-called 'exo-loop' which is found only in exo-acting enzymes in this family <cite>Yaoi2004</cite>. A crystal structure of a complex with xyloglucan-derived oligosaccharides elucidated the interaction with the side-chains of the substrate by these enzymes <cite>Martinez-Fleites2006</cite>. A number of GH74 complexes with large xyloglucan oligosaccharides is now known <cite>Arnal2019</cite>.
 == Family Firsts ==
@@ Line 59: / Line 59: @@
 #Chhabra2002 pmid=12417345
 #Takada1999 Takada G, Kawagushi T, Yoneda T, Kawasaki M, Sumitani JI, and Arai M. ''Molecular cloning and expression of the celluloytic system of Aspergillus aculeatus'', p. 364-373. ''In'' Ohmiya K, Hayashi K, Sakka K, Kobayashi Y, Karita S, and Kimura T (ed.), ''Genetics, biochemistry and ecology of cellulose degradation.'' 1999 Uni Publishers, Tokyo, Japan, ISBN 4-946450-17-3.
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH074]]

@@ Line 35: / Line 35: @@
 == Catalytic Residues ==
-Crystal structure of OXG-RCBH demonstrated that Asp35 and Asp465 are located in the middle of the binding cleft, and their crucial roles in hydrolytic activity were experimentally confirmed by site-directed mutagenesis <cite>Yaoi2004</cite>. However, their identities as [[general acid]] and [[general base]] were not assigned. The corresponding Asp residues in [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1515 ''Clostridium thermocellum''] xyloglucanase are nicely located between [[Sub-site nomenclature|subsites]] -1 and +1 in the complex structure with xyloglucan-derived oligosaccharides <cite>Martinez-Fleites2006</cite>.
+Crystal structure of OXG-RCBH demonstrated that Asp35 and Asp465 are located in the middle of the binding cleft, and their crucial roles in hydrolytic activity were experimentally confirmed by site-directed mutagenesis <cite>Yaoi2004</cite>. However, their identities as [[general acid]] and [[general base]] were not assigned. The corresponding Asp residues in Xgh74A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1515 ''Clostridium thermocellum''] are nicely located between [[Sub-site nomenclature|subsites]] -1 and +1 in the complex structure with xyloglucan-derived oligosaccharides <cite>Martinez-Fleites2006</cite>.
 == Three-dimensional structures ==

@@ Line 43: / Line 43: @@
 ;First stereochemistry determination:Xeg74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2021 ''Thermobifida fusca''] by <sup>1</sup>H-NMR <cite>Irwin2003</cite>.
 ;First gene cloning:The first gene cloned was AviIII from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=5053 ''Aspergillus aculeatus''] <cite>Takada1999</cite>, and the first xyloglucanase activity was confirmed by the study on EglC from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=5061 ''Aspergillus niger''] <cite>Hasper2002</cite>.
-;First [[general acid]] residue identification: OXG-RCBH from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=203496 ''Geotrichum sp. M128''] <cite>Yaoi2004</cite>.
+;First [[general acid]] residue identification: Xgh74A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1515 ''Clostridium thermocellum''] <cite>Martinez-Fleites2006</cite>.
-;First [[general base]] residue identification: OXG-RCBH from  [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=203496 ''Geotrichum sp. M128''] <cite>Yaoi2004</cite>.
+;First [[general base]] residue identification: Xgh74A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1515 ''Clostridium thermocellum''] <cite>Martinez-Fleites2006</cite>.
 ;First 3-D structure: OXG-RCBH from  [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=203496 ''Geotrichum sp. M128''] <cite>Yaoi2004</cite>.

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 == Kinetics and Mechanism ==
-Family 74 enzymes are [[inverting]] enzymes, as shown by NMR analysis on Xeg74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2021 ''Thermobifida fusca''] <cite>Irwin2003</cite> and XEG from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=203496 ''Geotrichum sp. M128''] <cite>Yaoi2004a</cite>.
+Family 74 enzymes are [[inverting]] enzymes, as shown by NMR analysis on Xeg74 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2021 ''Thermobifida fusca''] <cite>Irwin2003</cite>.
 == Catalytic Residues ==
@@ Line 52: / Line 52: @@
 #Yaoi2002 pmid=12374797
 #Irwin2003 pmid=12846842
-#Yaoi2004a pmid=14987996
+#Yaoi2004 pmid=15242597
 #Martinez-Fleites2006 pmid=16772298
 #York1993 pmid=8252539