Glycoside Hydrolase Family 188 - Revision history

Harry Brumer: /* Substrate specificities */ Added EC link

2023-12-19T17:33:17Z

Substrate specificities: Added EC link

Harry Brumer: /* Three-dimensional structures */ Added PDB links

2023-12-19T17:31:32Z

Three-dimensional structures: Added PDB links

Harry Brumer: /* Kinetics and Mechanism */

2023-12-19T17:27:42Z

Kinetics and Mechanism

Spencer Williams at 02:56, 18 December 2023

2023-12-18T02:56:32Z

Spencer Williams at 22:53, 17 December 2023

2023-12-17T22:53:09Z

Spencer Williams at 22:52, 17 December 2023

2023-12-17T22:52:52Z

Spencer Williams at 21:22, 17 December 2023

2023-12-17T21:22:22Z

Spencer Williams at 21:18, 17 December 2023

2023-12-17T21:18:30Z

Spencer Williams at 21:17, 17 December 2023

2023-12-17T21:17:24Z

Harry Brumer: Created page with " {{UnderConstruct..."

2023-12-17T20:13:54Z

Created page with " {{UnderConstruct..."

New page

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: [[User:Spencer Williams|Spencer Williams]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH188'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|retaining/inverting
|-
|'''Active site residues'''
|known/not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH188.html
|}
</div>


== Substrate specificities ==
Content is to be added here.

Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''

In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.

== Kinetics and Mechanism ==
Content is to be added here.

== Catalytic Residues ==
Content is to be added here.

== Three-dimensional structures ==
Content is to be added here.

== Family Firsts ==
;First stereochemistry determination: Content is to be added here.
;First catalytic nucleophile identification: Content is to be added here.
;First general acid/base residue identification: Content is to be added here.
;First 3-D structure: Content is to be added here.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [https://doi.org/10.1042/BIO03004026 DOI:10.1042/BIO03004026].
</biblio>


[[Category:Glycoside Hydrolase Families|GH188]]

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-The [[glycoside hydrolases]] of this family are found in bacteria, algae, plants and a small number of archaea <cite>#Kaur2024</cite>.  The family contains enzymes with sulfoquinovosidase activity (EC 3.2.1.199), namely the ability to cleave glycosides of 6-deoxy-6-sulfoquinovose. Sulfoquinovosidases are also found in family [[GH31]] <cite>#Speciale2016</cite>. Enzymes of this family have the ability to cleave both &alpha;- and &beta;-glycosides, and are dependent on an NAD<sup>+</sup> cofactor. Sulfoquinovosidases hydrolyse glycosides of sulfoquinovose such as sulfoquinovosyl glycerol, and liberate free sulfoquinovose, which can be used as a substrate in bacterial sulfoglycolysis and sulfoquinovose sulfolysis pathways <cite>#Snow2021</cite>.
+The [[glycoside hydrolases]] of this family are found in bacteria, algae, plants and a small number of archaea <cite>#Kaur2024</cite>.  The family contains enzymes with sulfoquinovosidase activity (EC [{{EClink}}3.2.1.199 3.2.1.199]), namely the ability to cleave glycosides of 6-deoxy-6-sulfoquinovose. Sulfoquinovosidases are also found in family [[GH31]] <cite>#Speciale2016</cite>. Enzymes of this family have the ability to cleave both &alpha;- and &beta;-glycosides, and are dependent on an NAD<sup>+</sup> cofactor. Sulfoquinovosidases hydrolyse glycosides of sulfoquinovose such as sulfoquinovosyl glycerol, and liberate free sulfoquinovose, which can be used as a substrate in bacterial sulfoglycolysis and sulfoquinovose sulfolysis pathways <cite>#Snow2021</cite>.
 == Kinetics and Mechanism ==

@@ Line 38: / Line 38: @@
 == Three-dimensional structures ==
-Crystallographic data is available for at least two GH188 enzymes, including as complexes with NADH, and NADH plus sulfoquinovose.  The 3D X-ray crystal structures include those of ''Flavobacterium'' sp. strain K172 SqgA (PDB 8QC8, 8QC2) and ''Arthrobacter'' sp. strain U41 SqgA (PDB 8QC3, 8QC6. 8QC5) <cite>#Kaur2024</cite>.  Each enzyme possesses an N-terminal dinucleotide-binding Rossman fold. The GH188 enzymes show structural similarities to inositol-2-dehydrogenase, glucose-fructose/IDH/MocA-like oxidoreductase, and NAD<sup>+</sup>-dependent ''N''-acetylgalactosaminidase of family [[GH109]].
+Crystallographic data is available for at least two GH188 enzymes, including as complexes with NADH, and NADH plus sulfoquinovose.  The 3D X-ray crystal structures include those of ''Flavobacterium'' sp. strain K172 SqgA (PDB [{{PDBlink}}8QC8 8QC8], [{{PDBlink}}8QC2 8QC2]) and ''Arthrobacter'' sp. strain U41 SqgA (PDB [{{PDBlink}}8QC3 8QC3], [{{PDBlink}}8QC6 8QC6], [{{PDBlink}}8QC5 8QC5]) <cite>#Kaur2024</cite>.  Each enzyme possesses an N-terminal dinucleotide-binding Rossman fold. The GH188 enzymes show structural similarities to inositol-2-dehydrogenase, glucose-fructose/IDH/MocA-like oxidoreductase, and NAD<sup>+</sup>-dependent ''N''-acetylgalactosaminidase of family [[GH109]].
 == Family Firsts ==

@@ Line 32: / Line 32: @@
 == Kinetics and Mechanism ==
-GH188 enzymes utilize an [[NAD-dependent hydrolysis]] mechanism that proceeds through oxidation-elimination-addition-reduction steps.  Exchange of the substrate C2 proton with solvent deuterium during the enzyme-catalyzed reaction was demonstrated by mass spectrometry <cite>#Kaur2024</cite>. The following chemical mechanism is proposed: (1) C3 hydride abstraction via the reduction of NAD<sup>+</sup> cofactor to NADH and simultaneous oxidation of the C3 hydroxyl group; (2) &alpha; to the ketone functionality, the C2 proton is deprotonated by a general catalytic base residue; (3) cleavage of the C1-O1 bond occurs in an &alpha;,&beta;-elimination, producing an &alpha;,&beta;-unsaturated ketone [[intermediate]]; (4) 1,4-Michael-like addition of a water molecule at C1; and (5) reduction of the C3 carbonyl functionality by the enzyme-bound NADH generates the product. Similar mechanisms are used in families [[GH4]], [[GH109]], [[GH177]] and [[GH179]].
+GH188 enzymes utilize an [[NAD-dependent hydrolysis]] mechanism that proceeds through oxidation-elimination-addition-reduction steps.  Exchange of the substrate C2 proton with solvent deuterium during the enzyme-catalyzed reaction was demonstrated by mass spectrometry <cite>#Kaur2024</cite>. The following chemical mechanism is proposed: (1) C3 hydride abstraction via the reduction of NAD<sup>+</sup> cofactor to NADH and simultaneous oxidation of the C3 hydroxyl group; (2) &alpha; to the ketone functionality, the C2 proton is deprotonated by a general catalytic base residue; (3) cleavage of the C1-O1 bond occurs in an &alpha;,&beta;-elimination, producing an &alpha;,&beta;-unsaturated ketone [[intermediate]]; (4) 1,4-Michael-like addition of a water molecule at C1; and (5) reduction of the C3 carbonyl functionality by the enzyme-bound NADH generates the product. Similar mechanisms are used in families [[GH4]], [[GH109]], [[GH177]], and [[GH179]].
 == Catalytic Residues ==

@@ Line 35: / Line 35: @@
 == Catalytic Residues ==
-Catalytic residues can be inferred on the basis of X-ray crystallographic data for complexes of GH188 enzymes with NAD<sup>+</sup> and sulfoquinovose <cite>#Kaur2024</cite>.  Tyr136 in ''Arthrobacter'' sp. strain U41 SqgA is conserved in all family GH188 members and is located close to C2-OH, suggesting a possible role as a [[general base]].  His321 is located close to the C1-OH and may act as [[general acid]] (along with Tyr136) for the glycosidic oxygen facilitating glycosidic bond scission. The sulfonate group is recognized by a triad of amino acids: one oxygen H-bonds to Arg166 (2.6 Å), a second to Lys172 (2.9 Å), and a third to the backbone amide of Leu170 (2.8 Å).
+Catalytic residues can be inferred on the basis of X-ray crystallographic data for complexes of GH188 enzymes with NAD<sup>+</sup> and sulfoquinovose <cite>#Kaur2024</cite>.  Tyr136 in ''Arthrobacter'' sp. strain U41 SqgA is conserved in most family GH188 members and is located close to C2-OH, suggesting a possible role as a [[general base]].  His321 is located close to the C1-OH and may act as [[general acid]] (along with Tyr136) for the glycosidic oxygen facilitating glycosidic bond scission. The sulfonate group is recognized by a triad of amino acids: one oxygen H-bonds to Arg166 (2.6 Å), a second to Lys172 (2.9 Å), and a third to the backbone amide of Leu170 (2.8 Å).
 == Three-dimensional structures ==

@@ Line 32: / Line 32: @@
 == Kinetics and Mechanism ==
-GH188 enzymes utilize an [[NAD-dependent hydrolysis]] mechanism that proceeds through oxidation-elimination-addition-reduction steps.  Exchange of the substrate C2 proton with solvent deuterium during the enzyme-catalyzed reaction was demonstrated by mass spectrometry <cite>#Kaur2024</cite>. The following chemical mechanism is proposed: (1) C3 hydride abstraction via the reduction of NAD<sup>+</sup> cofactor to NADH and simultaneous oxidation of the C3 hydroxyl group; (2) &alpha; to the ketone functionality, the C2 proton is deprotonated by a general catalytic base residue; (3) cleavage of the C1-O1 bond occurs in an &alpha;,&beta;-elimination, producing an &alpha;,&beta;-unsaturated ketone [[intermediate]]; (4) 1,4-Michael-like addition of a water molecule at C1; and (5) reduction of the C3 carbonyl functionality by the enzyme-bound NADH generates the product.
+GH188 enzymes utilize an [[NAD-dependent hydrolysis]] mechanism that proceeds through oxidation-elimination-addition-reduction steps.  Exchange of the substrate C2 proton with solvent deuterium during the enzyme-catalyzed reaction was demonstrated by mass spectrometry <cite>#Kaur2024</cite>. The following chemical mechanism is proposed: (1) C3 hydride abstraction via the reduction of NAD<sup>+</sup> cofactor to NADH and simultaneous oxidation of the C3 hydroxyl group; (2) &alpha; to the ketone functionality, the C2 proton is deprotonated by a general catalytic base residue; (3) cleavage of the C1-O1 bond occurs in an &alpha;,&beta;-elimination, producing an &alpha;,&beta;-unsaturated ketone [[intermediate]]; (4) 1,4-Michael-like addition of a water molecule at C1; and (5) reduction of the C3 carbonyl functionality by the enzyme-bound NADH generates the product. Similar mechanisms are used in families [[GH4]], [[GH109]], [[GH177]] and [[GH179]].
 == Catalytic Residues ==

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]:
+* [[Author]]: [[User:Spencer Williams|Spencer Williams]]
 * [[Responsible Curator]]:  [[User:Spencer Williams|Spencer Williams]]
 ----

← Older revision		Revision as of 21:18, 17 December 2023
Line 50:		Line 50:
	:''Flavobacterium'' sp. strain K172 SqgA <cite>#Kaur2024</cite>		:''Flavobacterium'' sp. strain K172 SqgA <cite>#Kaur2024</cite>

		+	==References==
		+	<biblio>
	#Kaur2024 pmid=38100472		#Kaur2024 pmid=38100472

@@ Line 15: / Line 15: @@
 |-
 |'''Mechanism'''
-|retaining/inverting
+|NAD-dependent hydrolysis
 |-
 |'''Active site residues'''
-|known/not known
+|known
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-Content is to be added here.
+The [[glycoside hydrolases]] of this family are found in bacteria, algae, plants and a small number of archaea <cite>#Kaur2024</cite>.  The family contains enzymes with sulfoquinovosidase activity (EC 3.2.1.199), namely the ability to cleave glycosides of 6-deoxy-6-sulfoquinovose. Sulfoquinovosidases are also found in family [[GH31]] <cite>#Speciale2016</cite>. Enzymes of this family have the ability to cleave both &alpha;- and &beta;-glycosides, and are dependent on an NAD<sup>+</sup> cofactor.
 == Kinetics and Mechanism ==
-Content is to be added here.
+GH188 enzymes utilize an [[NAD-dependent hydrolysis]] mechanism that proceeds through oxidation-elimination-addition-reduction steps.  Exchange of the substrate C2 proton with solvent deuterium during the enzyme-catalyzed reaction was demonstrated by mass spectrometry <cite>#Kaur2024</cite>. The following chemical mechanism is proposed: (1) C3 hydride abstraction via the reduction of NAD<sup>+</sup> cofactor to NADH and simultaneous oxidation of the C3 hydroxyl group; (2) &alpha; to the ketone functionality, the C2 proton is deprotonated by a general catalytic base residue; (3) cleavage of the C1-O1 bond occurs in an &alpha;,&beta;-elimination, producing an &alpha;,&beta;-unsaturated ketone [[intermediate]]; (4) 1,4-Michael-like addition of a water molecule at C1; and (5) reduction of the C3 carbonyl functionality by the enzyme-bound NADH generates the product.
 == Catalytic Residues ==
-Content is to be added here.
+Catalytic residues can be inferred on the basis of X-ray crystallographic data for complexes of GH188 enzymes with NAD<sup>+</sup> and sulfoquinovose <cite>#Kaur2024</cite>.  Tyr136 in ''Arthrobacter'' sp. strain U41 SqgA is conserved in all family GH188 members and is located close to C2-OH, suggesting a possible role as a [[general base]].  His321 is located close to the C1-OH and may act as [[general acid]] (along with Tyr136) for the glycosidic oxygen facilitating glycosidic bond scission. The sulfonate group is recognized by a triad of amino acids: one oxygen H-bonds to Arg166 (2.6 Å), a second to Lys172 (2.9 Å), and a third to the backbone amide of Leu170 (2.8 Å).
 == Three-dimensional structures ==
-Content is to be added here.
+Crystallographic data is available for at least two GH188 enzymes, including as complexes with NADH, and NADH plus sulfoquinovose.  The 3D X-ray crystal structures include those of ''Flavobacterium'' sp. strain K172 SqgA (PDB 8QC8, 8QC2) and ''Arthrobacter'' sp. strain U41 SqgA (PDB 8QC3, 8QC6. 8QC5) <cite>#Kaur2024</cite>.  Each enzyme possesses an N-terminal dinucleotide-binding Rossman fold. The GH188 enzymes show structural similarities to inositol-2-dehydrogenase, glucose-fructose/IDH/MocA-like oxidoreductase, and NAD<sup>+</sup>-dependent ''N''-acetylgalactosaminidase of family [[GH109]].
 == Family Firsts ==
-;First stereochemistry determination: Content is to be added here.
+;'''First stereochemistry determination
-;First catalytic nucleophile identification: Content is to be added here.
+:not applicable
-;First general acid/base residue identification: Content is to be added here.
+; '''First catalytic residue identification'''
-;First 3-D structure: Content is to be added here.
+:''Arthrobacter'' sp. strain U41 SqgA using 3D X-ray crystal structure <cite>#Kaur2024</cite>
-== References ==
+#Speciale2016 pmid=26878550
 </biblio>
 <!-- Do not delete this Category tag -->
 [[Category:Glycoside Hydrolase Families|GH188]]