Glycoside Hydrolase Family 125 - Revision history

Harry Brumer: Text replacement - "User:Alisdair Boraston" to "User:Al Boraston"

2021-12-18T21:38:23Z

Text replacement - "User:Alisdair Boraston" to "User:Al Boraston"

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

2021-12-18T21:17:04Z

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

Spencer Williams at 21:35, 23 January 2017

2017-01-23T21:35:07Z

Spencer Williams at 03:03, 22 January 2017

2017-01-22T03:03:07Z

Harry Brumer: Corrected 2p0v PDB ID

2016-11-08T23:09:22Z

Corrected 2p0v PDB ID

Spencer Williams: /* Catalytic Residues */

2012-11-26T01:48:05Z

Catalytic Residues

Spencer Williams at 10:54, 20 November 2012

2012-11-20T10:54:22Z

Harry Brumer at 23:30, 16 November 2012

2012-11-16T23:30:35Z

Al Boraston at 21:50, 16 November 2012

2012-11-16T21:50:30Z

Al Boraston at 21:49, 16 November 2012

2012-11-16T21:49:34Z

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: [[User:Alisdair Boraston|Alisdair Boraston]]
+* [[Author]]: [[User:Al Boraston|Alisdair Boraston]]
-* [[Responsible Curator]]:  [[User:Alisdair Boraston|Alisdair Boraston]]
+* [[Responsible Curator]]:  [[User:Al Boraston|Alisdair Boraston]]
 ----

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Alisdair Boraston^^^
+* [[Author]]: [[User:Alisdair Boraston|Alisdair Boraston]]
-* [[Responsible Curator]]:  ^^^Alisdair Boraston^^^
+* [[Responsible Curator]]:  [[User:Alisdair Boraston|Alisdair Boraston]]
 ----

@@ Line 33: / Line 33: @@
 == Kinetics and Mechanism ==
-Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with [[inverting|inversion]] of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.
+Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with [[inverting|inversion]] of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>. Crystallographic evidence from a binary complex of CpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose, complemented by quantum mechanics/molecular mechanics calculations of preferred conformations on-enzyme and of reaction coordinate metadynamics, supports a <sup>1</sup>''S''<sub>5</sub>&rarr;''B''<sub>2,5</sub><sup>‡</sup>&rarr;<sup>O</sup>''S''<sub>2</sub> conformational reaction coordinate <cite>Alonso-Gil2017</cite>.
 == Catalytic Residues ==
@@ Line 50: / Line 50: @@
 <biblio>
 #Gregg2011 pmid=21388958
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH125]]

@@ Line 39: / Line 39: @@
 == Three-dimensional structures ==
-The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provided insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provided a view of how more extensive substrates may be recognized by these enzymes.  The uncomplexed structures of two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2p0v 2p0v]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes and at present remain otherwise uncharacterized.
+The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable substrate analogue methyl 1,6-α-thiomannobiose provided insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provided a view of how more extensive substrates may be recognized by these enzymes.  The uncomplexed structures of two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2p0v 2p0v]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes and at present remain otherwise uncharacterized.
 == Family Firsts ==

@@ Line 39: / Line 39: @@
 == Three-dimensional structures ==
-The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provided insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provided a view of how more extensive substrates may be recognized by these enzymes.  The uncomplexed structures of two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes and at present remain otherwise uncharacterized.
+The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provided insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provided a view of how more extensive substrates may be recognized by these enzymes.  The uncomplexed structures of two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2p0v 2p0v]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes and at present remain otherwise uncharacterized.
 == Family Firsts ==
@@ Line 45: / Line 45: @@
 ;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.
 ;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.
-;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins  ([{{PDBlink}}3on6 3on6], [{{PDBlink}}3p2c 3p2c], and [{{PDBlink}}2pov 2pov]). These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.
+;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins  ([{{PDBlink}}3on6 3on6], [{{PDBlink}}3p2c 3p2c], and [{{PDBlink}}2p0v 2p0v]). These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.
 == References ==

@@ Line 36: / Line 36: @@
 == Catalytic Residues ==
-The structural analysis of CpGH125 suggested it uses aspartate 220 as a catalytic [[general acid]] and glutamate 393 as catalytic [[general base]]. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of [[Clan]] GH-L, specifically [[GH15]] and [[GH65]], which revealed conservation of these catalytic residues among all of the clan members.
+The structural analysis of CpGH125 suggested it uses aspartate 220 as a catalytic [[general acid]] and glutamate 393 as catalytic [[general base]]. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl ''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of [[Clan]] GH-L, specifically [[GH15]] and [[GH65]], which revealed conservation of these catalytic residues among all of the clan members.
 == Three-dimensional structures ==

@@ Line 30: / Line 30: @@
 == Substrate specificities ==
-The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.
+Family 125 [[glycoside hydrolases]], which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.
 == Kinetics and Mechanism ==
-Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.
+Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with [[inverting|inversion]] of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.
 == Catalytic Residues ==
-The structural analysis of CpGH125 suggested it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of [[Clan]] GH-L, specifically [[GH15]] and [[GH65]], which revealed conservation of these catalytic residues among all of the clan members.
+The structural analysis of CpGH125 suggested it uses aspartate 220 as a catalytic [[general acid]] and glutamate 393 as catalytic [[general base]]. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of [[Clan]] GH-L, specifically [[GH15]] and [[GH65]], which revealed conservation of these catalytic residues among all of the clan members.
 == Three-dimensional structures ==
@@ Line 42: / Line 42: @@
 == Family Firsts ==
-;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry  <cite>Gregg2011</cite>.
+;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with [[inverting|inversion]] of stereochemistry  <cite>Gregg2011</cite>.
 ;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.
 ;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.

← Older revision		Revision as of 21:50, 16 November 2012
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	== Three-dimensional structures ==		== Three-dimensional structures ==
−	The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provided insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provided a view of how more extensive substrates may be recognized by these enzymes. The uncomplexed structures two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes.	+	The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provided insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provided a view of how more extensive substrates may be recognized by these enzymes. The uncomplexed structures of two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes and at present remain otherwise uncharacterized.

@@ Line 37: / Line 37: @@
 == Catalytic Residues ==
-The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of Clan GH-L, specifically GH15 and GH65, which revealed conservation of these catalytic residues among all of the clan members.
+The structural analysis of CpGH125 suggested it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of Clan GH-L, specifically GH15 and GH65, which revealed conservation of these catalytic residues among all of the clan members.
 == Three-dimensional structures ==
-The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and reveal the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provide insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provides a view of how more extensive substrates may be recognized by these enzymes.  The uncomplexed structures two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes.
+The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provided insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provided a view of how more extensive substrates may be recognized by these enzymes.  The uncomplexed structures two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes.