Glycoside Hydrolase Family 62 - Revision history

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

2021-12-18T21:18:34Z

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

Harry Brumer: Identities of catalytic residues corrected according to Maehara et al. and comparable literature on GH43 (Shallom...Shoham, Biochemistry 2005)

2020-08-10T16:54:05Z

Identities of catalytic residues corrected according to Maehara et al. and comparable literature on GH43 (Shallom...Shoham, Biochemistry 2005)

Casper Wilkens at 08:36, 22 May 2019

2019-05-22T08:36:28Z

Casper Wilkens at 08:35, 22 May 2019

2019-05-22T08:35:53Z

Casper Wilkens at 08:34, 22 May 2019

2019-05-22T08:34:28Z

Casper Wilkens at 07:44, 27 September 2018

2018-09-27T07:44:00Z

Casper Wilkens at 07:42, 27 September 2018

2018-09-27T07:42:48Z

Casper Wilkens at 09:24, 21 September 2018

2018-09-21T09:24:53Z

Casper Wilkens at 09:22, 21 September 2018

2018-09-21T09:22:08Z

Casper Wilkens at 09:20, 21 September 2018

2018-09-21T09:20:02Z

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: [[User:Harry Gilbert|Harry Gilbert]] and ^^^Casper Wilkens^^^
+* [[Author]]: [[User:Harry Gilbert|Harry Gilbert]] and [[User:Casper Wilkens|Casper Wilkens]]
 * [[Responsible Curator]]:  [[User:Harry Gilbert|Harry Gilbert]]
 ----

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 == Catalytic Residues ==
-Asp ([[general acid]]) and Glu ([[general base]]), as suggested by tertiary structures <cite>Maehara2014 Siguier2014 Wang2014</cite> and supported by site-directed mutagenesis and kinetic data <cite>Maehara2014 Wang2014</cite>.
+Asp ([[general base]]) and Glu ([[general acid]]), as suggested by tertiary structures <cite>Maehara2014 Siguier2014 Wang2014</cite> and supported by site-directed mutagenesis and kinetic data <cite>Maehara2014 Wang2014</cite>.
 == Three-dimensional structures ==

@@ Line 33: / Line 33: @@
 == Three-dimensional structures ==
-Based on its location in [[clan]] F together with [[GH43]], enzymes from family GH62s were predicted to display a 5-fold &beta;-propeller fold. This hypothesis was confirmed by three papers published in 2014 <cite>Maehara2014 Siguier2014 Wang2014</cite>. The predicted catalytic general acid, catalytic general base and pKa modulator <cite>Vincent1997</cite> were also confirmed by mutagenesis data <cite>Maehara2014 Wang2014</cite>. The active site arabinose-containing pocket opens up into a cleft or channel that binds the xylooligosaccharides and thus the xylan chain. The residues that interact with the substrate backbone were identified for ''Streptomyces coelicolor'' &alpha;-L-arabinofuranosidase A (ScAbf62A) in a crystal structure in complex with xylopentaose, which spanned subsite +2R to +4NR  <cite>Maehara2014</cite>. In this respect a conserved tyrosine, present on a mobile loop,  was shown to make an important contribution to substrate binding through hydrophobic interactions with the arabinose located in the active site <cite>Contesini2017</cite>. Remarkably, the xylan main chain bound in two orientations in the crystal structures of ScAbf62A and ''Streptomyces thermoviolaceus'' &alpha;-L-arabinofuranosidase A, as may be required to position both single &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains in subsite -1 for productive binding in the active site pocket <cite>Maehara2014 Wang2014</cite>. The preference for either &alpha;-1,2 or &alpha;-1,3-L-arabinofuranose side chains seems to correlate with the presence of an arginine residue interacting with the xylan manin chain at the +2R subsite <cite>Sarch2019</cite>.
+Based on its location in [[clan]] F together with [[GH43]], enzymes from family GH62s were predicted to display a 5-fold &beta;-propeller fold. This hypothesis was confirmed by three papers published in 2014 <cite>Maehara2014 Siguier2014 Wang2014</cite>. The predicted catalytic general acid, catalytic general base and pKa modulator <cite>Vincent1997</cite> were also confirmed by mutagenesis data <cite>Maehara2014 Wang2014</cite>. The active site arabinose-containing pocket opens up into a cleft or channel that binds the xylooligosaccharides and thus the xylan chain. The residues that interact with the substrate backbone were identified for ''Streptomyces coelicolor'' &alpha;-L-arabinofuranosidase A (ScAbf62A) in a crystal structure in complex with xylopentaose, which spanned subsite +2R to +4NR  <cite>Maehara2014</cite>. In this respect a conserved tyrosine, present on a mobile loop,  was shown to make an important contribution to substrate binding through hydrophobic interactions with the arabinose located in the active site <cite>Contesini2017</cite>. Remarkably, the xylan main chain bound in two orientations in the crystal structures of ScAbf62A and ''Streptomyces thermoviolaceus'' &alpha;-L-arabinofuranosidase A, as may be required to position both single &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains in subsite -1 for productive binding in the active site pocket <cite>Maehara2014 Wang2014</cite>. The preference for either &alpha;-1,2 or &alpha;-1,3-L-arabinofuranose side chains seems to correlate with the presence of an arginine residue interacting with the xylan main chain at the +2R subsite <cite>Sarch2019</cite>.
 == Family Firsts ==

@@ Line 25: / Line 25: @@
 == Substrate specificities ==
-This small family of [[glycoside hydrolases]] comprises both eukaryotic and prokaryotic enzymes. All the characterized enzymes in this family are arabinofuranosidases and the majority act on xylose moieties in xylan and arabinose moieties in arabinan that are single substituted with &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains <cite>Wilkens2017</cite> with ''K''<sub>cat</sub> ranging from 0.3 to 180 s<sup>-1</sup> on wheat arabinoxylan <cite>Maehara2014 Wang2014 Wilkens2016</cite>. Interestlingly, the preference for &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains varies for GH62s <cite>Wilkens016 Sarch2019</cite>. However, a single GH62 enzyme from ''Pencillium oxalicum'' exclusively act on the &alpha;-1,3-L-arabinofuranose side chains <cite>Hu2018</cite>. The GH62 enzymes also display limited non-specific arabinofuranosidase activity; for example the arabinofuranosidases exhibit no <cite>Kellett1990</cite> or very little <cite>Maehara2014 Wang2014</cite> activity against 4-nitrophenyl &alpha;-L-arabinofuranoside. Several of these enzymes contain carbohydrate binding modules that target cellulose<cite>Kellett1990</cite> or xylan<cite>Dupont1998</cite>.
+This small family of [[glycoside hydrolases]] comprises both eukaryotic and prokaryotic enzymes. All the characterized enzymes in this family are arabinofuranosidases and the majority act on xylose moieties in xylan and arabinose moieties in arabinan that are single substituted with &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains <cite>Wilkens2017</cite> with ''K''<sub>cat</sub> ranging from 0.3 to 180 s<sup>-1</sup> on wheat arabinoxylan <cite>Maehara2014 Wang2014 Wilkens2016</cite>. Interestlingly, the preference for &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains varies for GH62s, hence the catalytic rate for the two side chains vary<cite>Wilkens016 Sarch2019</cite>. However, a single GH62 enzyme from ''Pencillium oxalicum'' exclusively act on the &alpha;-1,3-L-arabinofuranose side chains <cite>Hu2018</cite>. The GH62 enzymes also display limited non-specific arabinofuranosidase activity; for example the arabinofuranosidases exhibit no <cite>Kellett1990</cite> or very little <cite>Maehara2014 Wang2014</cite> activity against 4-nitrophenyl &alpha;-L-arabinofuranoside. Several of these enzymes contain carbohydrate binding modules that target cellulose<cite>Kellett1990</cite> or xylan<cite>Dupont1998</cite>.
 == Kinetics and Mechanism ==
 The stereochemical course of arabinose was followed by <sup>1</sup>H NMR during hydrolysis of a 50:50 mixture of XA<sup>2</sup>XX:XA<sup>3</sup>XX by ''Aspergillus nidulans'' &alpha;-L-arabinofuranosidase A, resulting in the release of &beta;-furanose demonstrating that GH62 enzymes in fact are [[inverting]] enzymes <cite>Wilkens2016</cite>, which is in accordance with the known inverting mechanism for [[GH43]] <cite>Pitson1996</cite> constituting [[clan]] F with GH62 <cite>Lombard2014</cite>. Due to arabinose's fast mutarotation, however, the anomeric signal decreased considerably already after 1 min, which was overcome by recording the first spectrum 23 s after enzyme addition <cite>Wilkens2016</cite>.

@@ Line 25: / Line 25: @@
 == Substrate specificities ==
-This small family of [[glycoside hydrolases]] comprises both eukaryotic and prokaryotic enzymes. All the characterized enzymes in this family are arabinofuranosidases and the majority act on xylose moieties in xylan and arabinose moieties in arabinan that are single substituted with &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains <cite>Wilkens2017</cite> with ''K''<sub>cat</sub> ranging from 0.3 to 180 s<sup>-1</sup> on wheat arabinoxylan <cite>Maehara2014 Wang2014 Wilkens2016</cite>. However, a single GH62 enzyme from ''Pencillium oxalicum'' exclusively act on the &alpha;-1,3-L-arabinofuranose side chains <cite>Hu2018</cite>. The GH62 enzymes also display limited non-specific arabinofuranosidase activity; for example the arabinofuranosidases exhibit no <cite>Kellett1990</cite> or very little <cite>Maehara2014 Wang2014</cite> activity against 4-nitrophenyl &alpha;-L-arabinofuranoside. Several of these enzymes contain carbohydrate binding modules that target cellulose<cite>Kellett1990</cite> or xylan<cite>Dupont1998</cite>.
+This small family of [[glycoside hydrolases]] comprises both eukaryotic and prokaryotic enzymes. All the characterized enzymes in this family are arabinofuranosidases and the majority act on xylose moieties in xylan and arabinose moieties in arabinan that are single substituted with &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains <cite>Wilkens2017</cite> with ''K''<sub>cat</sub> ranging from 0.3 to 180 s<sup>-1</sup> on wheat arabinoxylan <cite>Maehara2014 Wang2014 Wilkens2016</cite>. Interestlingly, the preference for &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains varies for GH62s <cite>Wilkens016 Sarch2019</cite>. However, a single GH62 enzyme from ''Pencillium oxalicum'' exclusively act on the &alpha;-1,3-L-arabinofuranose side chains <cite>Hu2018</cite>. The GH62 enzymes also display limited non-specific arabinofuranosidase activity; for example the arabinofuranosidases exhibit no <cite>Kellett1990</cite> or very little <cite>Maehara2014 Wang2014</cite> activity against 4-nitrophenyl &alpha;-L-arabinofuranoside. Several of these enzymes contain carbohydrate binding modules that target cellulose<cite>Kellett1990</cite> or xylan<cite>Dupont1998</cite>.
 == Kinetics and Mechanism ==
 The stereochemical course of arabinose was followed by <sup>1</sup>H NMR during hydrolysis of a 50:50 mixture of XA<sup>2</sup>XX:XA<sup>3</sup>XX by ''Aspergillus nidulans'' &alpha;-L-arabinofuranosidase A, resulting in the release of &beta;-furanose demonstrating that GH62 enzymes in fact are [[inverting]] enzymes <cite>Wilkens2016</cite>, which is in accordance with the known inverting mechanism for [[GH43]] <cite>Pitson1996</cite> constituting [[clan]] F with GH62 <cite>Lombard2014</cite>. Due to arabinose's fast mutarotation, however, the anomeric signal decreased considerably already after 1 min, which was overcome by recording the first spectrum 23 s after enzyme addition <cite>Wilkens2016</cite>.
@@ Line 33: / Line 33: @@
 == Three-dimensional structures ==
-Based on its location in [[clan]] F together with [[GH43]], enzymes from family GH62s were predicted to display a 5-fold &beta;-propeller fold. This hypothesis was confirmed by three papers published in 2014 <cite>Maehara2014 Siguier2014 Wang2014</cite>. The predicted catalytic general acid, catalytic general base and pKa modulator <cite>Vincent1997</cite> were also confirmed by mutagenesis data <cite>Maehara2014 Wang2014</cite>. The active site arabinose-containing pocket opens up into a cleft or channel that binds the xylooligosaccharides and thus the xylan chain. The residues that interact with the substrate backbone were identified for ''Streptomyces coelicolor'' &alpha;-L-arabinofuranosidase A (ScAbf62A) in a crystal structure in complex with xylopentaose, which spanned subsite +2R to +4NR  <cite>Maehara2014</cite>. In this respect a conserved tyrosine, present on a mobile loop,  was shown to make an important contribution to substrate binding through hydrophobic interactions with the arabinose located in the active site <cite>Contesini2017</cite>. Remarkably, the xylan main chain bound in two orientations in the crystal structures of ScAbf62A and ''Streptomyces thermoviolaceus'' &alpha;-L-arabinofuranosidase A, as may be required to position both single &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains in subsite -1 for productive binding in the active site pocket <cite>Maehara2014 Wang2014</cite>.
+Based on its location in [[clan]] F together with [[GH43]], enzymes from family GH62s were predicted to display a 5-fold &beta;-propeller fold. This hypothesis was confirmed by three papers published in 2014 <cite>Maehara2014 Siguier2014 Wang2014</cite>. The predicted catalytic general acid, catalytic general base and pKa modulator <cite>Vincent1997</cite> were also confirmed by mutagenesis data <cite>Maehara2014 Wang2014</cite>. The active site arabinose-containing pocket opens up into a cleft or channel that binds the xylooligosaccharides and thus the xylan chain. The residues that interact with the substrate backbone were identified for ''Streptomyces coelicolor'' &alpha;-L-arabinofuranosidase A (ScAbf62A) in a crystal structure in complex with xylopentaose, which spanned subsite +2R to +4NR  <cite>Maehara2014</cite>. In this respect a conserved tyrosine, present on a mobile loop,  was shown to make an important contribution to substrate binding through hydrophobic interactions with the arabinose located in the active site <cite>Contesini2017</cite>. Remarkably, the xylan main chain bound in two orientations in the crystal structures of ScAbf62A and ''Streptomyces thermoviolaceus'' &alpha;-L-arabinofuranosidase A, as may be required to position both single &alpha;-1,2 and &alpha;-1,3-L-arabinofuranose side chains in subsite -1 for productive binding in the active site pocket <cite>Maehara2014 Wang2014</cite>. The preference for either &alpha;-1,2 or &alpha;-1,3-L-arabinofuranose side chains seems to correlate with the presence of an arginine residue interacting with the xylan manin chain at the +2R subsite <cite>Sarch2019</cite>.
 == Family Firsts ==
@@ Line 55: / Line 55: @@
 #Hu2018 pmid=29611040
 #Pitson1996 pmid=8946944
-#Lombard2014 pmid=24270786
+#Sarch2019 pmid=30936018
 </biblio>
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 [[Category:Glycoside Hydrolase Families|GH062]]