Glycoside Hydrolase Family 120 - Revision history

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

2021-12-18T21:14:58Z

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

Spencer Williams at 11:21, 30 November 2016

2016-11-30T11:21:07Z

Spencer Williams at 05:23, 30 November 2016

2016-11-30T05:23:35Z

Spencer Williams at 02:09, 30 November 2016

2016-11-30T02:09:37Z

Harry Brumer: /* Three-dimensional structures */

2016-11-29T18:54:38Z

Three-dimensional structures

Harry Brumer: added some additional PDB links

2016-11-29T18:54:11Z

added some additional PDB links

Harry Brumer: changed PDB link to xylobiose complex

2016-11-29T18:51:02Z

changed PDB link to xylobiose complex

Harry Brumer: /* Catalytic Residues */

2016-11-29T18:21:23Z

Catalytic Residues

Harry Brumer: /* Kinetics and Mechanism */

2016-11-29T18:19:48Z

Kinetics and Mechanism

Harry Brumer at 18:17, 29 November 2016

2016-11-29T18:17:54Z

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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]]: ^^^Spencer Williams^^^
+* [[Author]]: [[User:Spencer Williams|Spencer Williams]]
-* [[Responsible Curator]]:  ^^^Spencer Williams^^^
+* [[Responsible Curator]]:  [[User:Spencer Williams|Spencer Williams]]
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 == Three-dimensional structures ==
-The three-dimensional structure has been solved for ''T. saccharolyticum'' XylC <cite>Huang2012</cite>. The protein consists of a &beta;-strand rich fold, which comprises two domains: a core domain that folds into a right-handed parallel &beta;-helix and a small flanking region that folds into a &beta;-sandwich domain. The overal fold displays similarity to members of polysaccharide lyase family 1 ([[PL1]]) and glycoside hydrolase family 28 ([[GH28]]). Separate complexes of XylC have been reported with Tris (PDB ID [{{PDBlink}}3vst  3vst]), xylose (PDB ID [{{PDBlink}}3vsv  3vsv]), and xylobiose (PDB ID [{{PDBlink}}3vsu  3vsu]); in all three complexes the ligands bind at a similar location assigned as the active site, which was located at the interface of the two &beta;-strand domains. Three conserved carboxylic acids, Asp382, Glu353 and Glu405, were identified located near the anomeric carbon of the xylose residue in the xylobiose and D-xylose complexes. The XylC-xylose complex revealed a large number of [[surface binding sites]]. Aside from the four xylose molecules bound at the putative active site, within the asymmetric unit tetramer, 31 other molecules were bound at sites located at the dimer interfaces within the asymmetric unit, and other surface sites.
+The three-dimensional structure has been solved for ''T. saccharolyticum'' XylC <cite>Huang2012</cite>. The protein consists of a &beta;-strand rich fold, which comprises two domains: a core domain that folds into a right-handed parallel &beta;-helix and a small flanking region that folds into a &beta;-sandwich domain. The overall fold displays similarity to members of polysaccharide lyase family 1 ([[PL1]]) and glycoside hydrolase family 28 ([[GH28]]). Separate complexes of XylC have been reported with Tris (PDB ID [{{PDBlink}}3vst  3vst]), xylose (PDB ID [{{PDBlink}}3vsv  3vsv]), and xylobiose (PDB ID [{{PDBlink}}3vsu  3vsu]); in all three complexes the ligands bind at a similar location assigned as the active site, which was located at the interface of the two &beta;-strand domains. Three conserved carboxylic acids, Asp382, Glu353 and Glu405, were identified located near the anomeric carbon of the xylose residue in the xylobiose and D-xylose complexes. The XylC-xylose complex revealed a large number of [[surface binding site]]s. Aside from the four xylose molecules bound at the putative active site, within the asymmetric unit tetramer, 31 other molecules were bound at sites located at the dimer interfaces within the asymmetric unit, and other surface sites.
 == Family Firsts ==

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family GH120 have been reported to possess &beta;-xylosidase activity. XylC from ''Thermoanaerobacterium saccharolyticum'' hydrolyzed xylobiose and xylotriose, to afford xylose <cite>Shao2011</cite>. No activity was detected on oat spelt or birch wood xylans. XylB from ''Bifidobacterium adolescentis'' possessed only weak activity on xylobiose, but much greater on higher oligomers from xylotriose through xylohexaose <cite>Laegart2011</cite>. XylB was shown to act to remove xylose residues from the non-reducing end of xylooligosaccharides and thus is an exo-xylosidase <cite>Laegart2011</cite>. Both ''T. saccharolyticum'' XylC and XylB from ''Bifidobacterium adolescentis'' can hydrolyze assorted aryl &beta;-xylosides <cite>Shao2011 Cecchini2015</cite>. XylB showed exceptionally weak activity on p-nitrophenyl-α-L-arabinofuranoside <cite>Laegart2011</cite>.
+[[Glycoside hydrolases]] of family GH120 have been reported to possess &beta;-xylosidase activity. XylC from ''Thermoanaerobacterium saccharolyticum'' hydrolyzed xylobiose and xylotriose, to afford xylose <cite>Shao2011</cite>. No activity was detected on oat spelt or birch wood xylans. XylB from ''Bifidobacterium adolescentis'' possessed only weak activity on xylobiose, but much greater on higher oligomers from xylotriose through xylohexaose <cite>Laegart2011</cite>. XylB was shown to act to remove xylose residues from the non-reducing end of xylooligosaccharides and thus is an exo-xylosidase <cite>Laegart2011</cite>. Both ''T. saccharolyticum'' XylC and ''B. adolescentis'' XylB  can hydrolyze assorted aryl &beta;-xylosides <cite>Shao2011 Cecchini2015</cite>. ''B. adolescentis'' XylB showed exceptionally weak activity on ''p''-nitrophenyl-α-L-arabinofuranoside <cite>Laegart2011</cite>; ''T. saccharolyticum'' XylC showed no detectable activity against this substrate <cite>Shao2011</cite>.
 == Kinetics and Mechanism ==

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of family GH120 have been reported to possess &beta;-xylosidase activity. XylC from ''Thermoanaerobacterium saccharolyticum'' hydrolyzed xylobiose and xylotriose, to afford xylose <cite>Shao2011</cite>. No activity was detected on oat spelt or birch wood xylans. Both ''T. saccharolyticum'' XylC and XylB from ''Bifidobacterium adolescentis'' can hydrolyze assorted aryl &beta;-xylosides <cite>Shao2011 Cecchini2015</cite>.
+[[Glycoside hydrolases]] of family GH120 have been reported to possess &beta;-xylosidase activity. XylC from ''Thermoanaerobacterium saccharolyticum'' hydrolyzed xylobiose and xylotriose, to afford xylose <cite>Shao2011</cite>. No activity was detected on oat spelt or birch wood xylans. XylB from ''Bifidobacterium adolescentis'' possessed only weak activity on xylobiose, but much greater on higher oligomers from xylotriose through xylohexaose <cite>Laegart2011</cite>. XylB was shown to act to remove xylose residues from the non-reducing end of xylooligosaccharides and thus is an exo-xylosidase <cite>Laegart2011</cite>. Both ''T. saccharolyticum'' XylC and XylB from ''Bifidobacterium adolescentis'' can hydrolyze assorted aryl &beta;-xylosides <cite>Shao2011 Cecchini2015</cite>. XylB showed exceptionally weak activity on p-nitrophenyl-α-L-arabinofuranoside <cite>Laegart2011</cite>.
 == Kinetics and Mechanism ==
@@ Line 38: / Line 38: @@
 == Three-dimensional structures ==
-The three-dimensional structure has been solved for ''T. saccharolyticum'' XylC <cite>Huang2012</cite>. The protein consists of a &beta;-strand rich fold, which comprises two domains: a core domain that folds into a right-handed parallel &beta;-helix and a small flanking region that folds into a &beta;-sandwich domain.  Separate complexes of XylC have been reported with Tris (PDB ID [{{PDBlink}}3vst  3vst]), xylose (PDB ID [{{PDBlink}}3vsv  3vsv]), and xylobiose (PDB ID [{{PDBlink}}3vsu  3vsu]); in all three complexes the ligands bind at a similar location assigned as the active site, which was located at the interface of the two &beta;-strand domains. Three conserved carboxylic acids, Asp382, Glu353 and Glu405, were identified located near the anomeric carbon of the xylose residue in the xylobiose and D-xylose complexes.
+The three-dimensional structure has been solved for ''T. saccharolyticum'' XylC <cite>Huang2012</cite>. The protein consists of a &beta;-strand rich fold, which comprises two domains: a core domain that folds into a right-handed parallel &beta;-helix and a small flanking region that folds into a &beta;-sandwich domain. The overal fold displays similarity to members of polysaccharide lyase family 1 ([[PL1]]) and glycoside hydrolase family 28 ([[GH28]]). Separate complexes of XylC have been reported with Tris (PDB ID [{{PDBlink}}3vst  3vst]), xylose (PDB ID [{{PDBlink}}3vsv  3vsv]), and xylobiose (PDB ID [{{PDBlink}}3vsu  3vsu]); in all three complexes the ligands bind at a similar location assigned as the active site, which was located at the interface of the two &beta;-strand domains. Three conserved carboxylic acids, Asp382, Glu353 and Glu405, were identified located near the anomeric carbon of the xylose residue in the xylobiose and D-xylose complexes. The XylC-xylose complex revealed a large number of [[surface binding sites]]. Aside from the four xylose molecules bound at the putative active site, within the asymmetric unit tetramer, 31 other molecules were bound at sites located at the dimer interfaces within the asymmetric unit, and other surface sites.
 == Family Firsts ==
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 #Shao2011 pmid=21131522
 #Cecchini2015 pmid=26297820
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH120]]

@@ Line 38: / Line 38: @@
 == Three-dimensional structures ==
-The three-dimensional structure has been solved for ''T. saccharolyticum'' XylC <cite>Huang2012</cite>. The protein consists of a &beta;-strand rich fold, which comprises two domains: a core domain that folds into a right-handed parallel &beta;-helix and a small flanking region that folds into a &beta;-sandwich domain.  Separate complexes of XylC have been reported with Tris (PDB ID [{{PDBlink}}3vst  3vst], xylose (PDB ID [{{PDBlink}}3vsv  3vsv], and xylobiose (PDB ID [{{PDBlink}}3vsu  3vsu]; in all three complexes the ligands bind at a similar location assigned as the active site, which was located at the interface of the two &beta;-strand domains. Three conserved carboxylic acids, Asp382, Glu353 and Glu405, were identified located near the anomeric carbon of the xylose residue in the xylobiose and D-xylose complexes.
+The three-dimensional structure has been solved for ''T. saccharolyticum'' XylC <cite>Huang2012</cite>. The protein consists of a &beta;-strand rich fold, which comprises two domains: a core domain that folds into a right-handed parallel &beta;-helix and a small flanking region that folds into a &beta;-sandwich domain.  Separate complexes of XylC have been reported with Tris (PDB ID [{{PDBlink}}3vst  3vst]), xylose (PDB ID [{{PDBlink}}3vsv  3vsv]), and xylobiose (PDB ID [{{PDBlink}}3vsu  3vsu]); in all three complexes the ligands bind at a similar location assigned as the active site, which was located at the interface of the two &beta;-strand domains. Three conserved carboxylic acids, Asp382, Glu353 and Glu405, were identified located near the anomeric carbon of the xylose residue in the xylobiose and D-xylose complexes.
 == Family Firsts ==

@@ Line 38: / Line 38: @@
 == Three-dimensional structures ==
-The three-dimensional structure has been solved for ''T. saccharolyticum'' XylC <cite>Huang2012</cite>. The protein consists of a &beta;-strand rich fold, which comprises two domains: a core domain that folds into a right-handed parallel &beta;-helix and a small flanking region that folds into a &beta;-sandwich domain.  Separate complexes of XylC have been reported with Tris, xylose and xylobiose; in all three complexes the ligands bind at a similar location assigned as the active site, which was located at the interface of the two &beta;-strand domains. Three conserved carboxylic acids, Asp382, Glu353 and Glu405, were identified located near the anomeric carbon of the xylose residue in the xylobiose and D-xylose complexes.
+The three-dimensional structure has been solved for ''T. saccharolyticum'' XylC <cite>Huang2012</cite>. The protein consists of a &beta;-strand rich fold, which comprises two domains: a core domain that folds into a right-handed parallel &beta;-helix and a small flanking region that folds into a &beta;-sandwich domain.  Separate complexes of XylC have been reported with Tris (PDB ID [{{PDBlink}}3vst  3vst], xylose (PDB ID [{{PDBlink}}3vsv  3vsv], and xylobiose (PDB ID [{{PDBlink}}3vsu  3vsu]; in all three complexes the ligands bind at a similar location assigned as the active site, which was located at the interface of the two &beta;-strand domains. Three conserved carboxylic acids, Asp382, Glu353 and Glu405, were identified located near the anomeric carbon of the xylose residue in the xylobiose and D-xylose complexes.
 == Family Firsts ==
@@ Line 44: / Line 44: @@
 ;First catalytic nucleophile identification: Assigned for ''T. saccharolyticum'' XylC on the basis of structural analysis, and mutagenesis <cite>Huang2012</cite>.
 ;First general acid/base residue identification: Assigned for ''Bifidobacterium adolescentis'' XylB by chemical rescue kinetics with azide <cite>Cecchini2015</cite>.
-;First 3-D structure: XylC from ''T. saccharolyticum'' (PDB ID [{{PDBlink}}3vsu  3vsu]) <cite>Huang2012</cite>.
+;First 3-D structure: XylC from ''T. saccharolyticum'' (''e.g.'' PDB ID [{{PDBlink}}3vsu  3vsu]) <cite>Huang2012</cite>.
 == References ==

@@ Line 35: / Line 35: @@
 == Catalytic Residues ==
-A three-dimensional X-ray structure of ''T. saccharolyticum'' XylC highlighted three conserved carboxylate residues, Asp382, Glu353 and Glu405,  located near the anomeric carbon of xylose and xylobiose bound in the putative active site <cite>Huang2012</cite>. Mutagenesis of these residues to alanine provided mutant proteins that were catalytically inactive <cite>Huang2012</cite>. On the basis of the relative orientation and distance from the anomeric centre, two of these residues were tentatively assigned as nucleophile (Asp382) and acid/base (Glu405) <cite>Huang2012</cite>. A more detailed mechanistic study was performed on ''B. adolescentis'' XylB <cite>Cecchini2015</cite>; for this protein Glu364, Asp393 and Glu416 correspond to Glu353, Asp382 and Glu405 in ''T. saccharolyticum'' XylC. Kinetic analysis of the alanine mutants at these three positions showed that the D393A mutant suffered the greatest loss in activity (10<sup>5</sup>-fold) using pNP-Xyl as substrate, which was partially restored in the D393E mutant, consistent with a role for Asp393 as nucleophile, and matching the role assigned for Asp382 in ''T. saccharolyticum'' XylC <cite>Cecchini2015</cite>. Glu416 was assigned as acid/base on the basis of a range of kinetic experiments including effects upon rate for mutants at this position for aryl xylosides with different leaving group abilities, and through chemical rescue of catalytic activity in the presence of azide <cite>Cecchini2015</cite>.
+A three-dimensional X-ray structure of ''T. saccharolyticum'' XylC highlighted three conserved carboxylate residues, Asp382, Glu353 and Glu405,  located near the anomeric carbon of xylose and xylobiose bound in the putative active site <cite>Huang2012</cite>. Mutagenesis of these residues to alanine provided mutant proteins that were catalytically inactive <cite>Huang2012</cite>. On the basis of the relative orientation and distance from the anomeric centre, two of these residues were tentatively assigned as the nucleophile (Asp382) and the general acid/base (Glu405) <cite>Huang2012</cite>. A more detailed mechanistic study was performed on ''B. adolescentis'' XylB <cite>Cecchini2015</cite>; for this protein Glu364, Asp393 and Glu416 correspond to Glu353, Asp382 and Glu405 in ''T. saccharolyticum'' XylC. Kinetic analysis of the alanine mutants at these three positions showed that the D393A mutant suffered the greatest loss in activity (10<sup>5</sup>-fold) using pNP-Xyl as substrate, which was partially restored in the D393E mutant, consistent with a role for Asp393 as nucleophile, and matching the role assigned for Asp382 in ''T. saccharolyticum'' XylC <cite>Cecchini2015</cite>. Glu416 was assigned as acid/base on the basis of a range of kinetic experiments including effects upon rate for mutants at this position for aryl xylosides with different leaving group abilities, and through chemical rescue of catalytic activity in the presence of azide <cite>Cecchini2015</cite>.
 == Three-dimensional structures ==

@@ Line 32: / Line 32: @@
 == Kinetics and Mechanism ==
-Incubation of XylC from ''T. saccharolyticum'' with 4-nitrophenyl &beta;-xyloside and alcohols including methanol, ethanol and 1-propanol resulted in the formation of the corresponding alkyl glycosides through transglycosidation <cite>Shao2011</cite>. The stereochemistry of 4-nitrophenyl &beta;-xyloside hydrolysis catalyzed by XylB from ''Bifidobacterium adolescentis'' was monitored by <sup>1</sup>H NMR spectroscopy and revealed the initial formation of the &beta;-anomer of xylose <cite>Cecchini2015</cite>. These data support the assignment of a [[retaining]] mechanism to these enzymes and the family, and is consistent with the enzyme utilizing a [[classical Koshland double-displacement mechanism]].
+Incubation of XylC from ''T. saccharolyticum'' with 4-nitrophenyl &beta;-xyloside and alcohols including methanol, ethanol and 1-propanol resulted in the formation of the corresponding alkyl glycosides through [[Transglycosylases|transglycosylation]] <cite>Shao2011</cite>. The stereochemistry of 4-nitrophenyl &beta;-xyloside hydrolysis catalyzed by XylB from ''Bifidobacterium adolescentis'' was monitored by <sup>1</sup>H NMR spectroscopy and revealed the initial formation of the &beta;-anomer of xylose <cite>Cecchini2015</cite>. These data support the assignment of a [[retaining]] mechanism to these enzymes and the family, and is consistent with the enzyme utilizing a [[classical Koshland double-displacement mechanism]].
 == Catalytic Residues ==