Glycoside Hydrolase Family 4 - Revision history

Spencer Williams at 02:35, 16 December 2023

2023-12-16T02:35:44Z

Spencer Williams at 02:35, 16 December 2023

2023-12-16T02:35:23Z

Spencer Williams at 02:22, 16 December 2023

2023-12-16T02:22:02Z

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

2021-12-18T21:17:04Z

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

Harry Brumer: added DOI for Koshland ref.

2019-07-17T17:31:41Z

added DOI for Koshland ref.

Harry Brumer: updated CAZyDBlink

2012-09-10T16:29:40Z

updated CAZyDBlink

Spencer Williams at 05:21, 11 August 2010

2010-08-11T05:21:33Z

Spencer Williams at 11:43, 14 June 2010

2010-06-14T11:43:28Z

Harry Brumer at 13:53, 8 November 2009

2009-11-08T13:53:04Z

Harry Brumer at 06:53, 6 October 2009

2009-10-06T06:53:08Z

@@ Line 27: / Line 27: @@
 ==Substrate specificities==
-The majority of the [[glycoside hydrolases]] of this family are of bacterial origin, but they have recently been found in the archaeal taxa <cite>#1</cite>.  Unlike other families of glycosidases, some of the enzymes in Family 4 possess distinct substrate specificities from each other<cite>#1 #2</cite>.  This family contains &alpha;-glucosidases, &alpha;-galactosidases, &alpha;-glucuronidases, 6-phospho-&alpha;-glucosidases, and 6-phospho-&beta;-glucosidases.  Similar to [[GH1]], some enzymes prefer phosphorylated substrates over non-phosphorylated substrates <cite>#2 #3</cite>.  Members of this family include both &alpha;- and &beta;-glycosidases.  The ability of a single enzyme to hydrolyze natural substrates of different anomeric configurations was first discovered in family GH4, and they were the first glycosidases that exhibited an absolute requirement for NAD<sup>+</sup> and a divalent metal ion and in some instances reducing environments for catalytic activity <cite>#4 #5 #6 #7 #8 #9 #10 #11</cite>.  The cofactors are proposed to play key mechanistic roles in the atypical glycosidase mechanism.  Unlike GH4, metal ions are required by some glycosidases for structural integrity <cite>#12 #13</cite> or proper configuration of an active enzyme <cite>#14 #15 #16 #17</cite>.  Meanwhile, GH4 is the first family of glycoside hydrolases reported to require a NAD<sup>+</sup>  cofactor for catalytic activity <cite>#4 #5 #6 #7 #8 #10 #11 #18 #19 #20 #21 #22</cite>.  Subsequently, enzymes of families [[GH109]], [[GH177]], [[GH179]], and [[GH188]] has been shown to also require a NAD<sup>+</sup> cofactor.  The hydrolysis of thioglycosides with activated leaving groups has been documented in GH84 <cite>#23</cite>, GH1 <cite>#24 #25 #26 #27 #28 #29</cite>.  However, GH4 is currently the only family that has been shown to catalyze the hydrolysis of unactivated thioglycoside substrates <cite>#30</cite>.  The remarkable substrate specificities are all feasible due to the &beta;-elimination mechanism discussed below.
+The majority of the [[glycoside hydrolases]] of this family are of bacterial origin, but they are also found in the archaeal taxa <cite>#1</cite>.  Unlike other families of glycosidases, some of the enzymes in Family 4 possess distinct substrate specificities from each other<cite>#1 #2</cite>.  This family contains &alpha;-glucosidases, &alpha;-galactosidases, &alpha;-glucuronidases, 6-phospho-&alpha;-glucosidases, and 6-phospho-&beta;-glucosidases.  Similar to [[GH1]], some enzymes prefer phosphorylated substrates over non-phosphorylated substrates <cite>#2 #3</cite>.  Members of this family include both &alpha;- and &beta;-glycosidases.  The ability of a single enzyme to hydrolyze natural substrates of different anomeric configurations was first discovered in family GH4, and they were the first glycosidases that exhibited an absolute requirement for NAD<sup>+</sup> and a divalent metal ion and in some instances reducing environments for catalytic activity <cite>#4 #5 #6 #7 #8 #9 #10 #11</cite>.  The cofactors are proposed to play key mechanistic roles in the atypical glycosidase mechanism.  Unlike GH4, metal ions are required by some glycosidases for structural integrity <cite>#12 #13</cite> or proper configuration of an active enzyme <cite>#14 #15 #16 #17</cite>.  Meanwhile, GH4 is the first family of glycoside hydrolases reported to require a NAD<sup>+</sup>  cofactor for catalytic activity <cite>#4 #5 #6 #7 #8 #10 #11 #18 #19 #20 #21 #22</cite>.  Subsequently, enzymes of families [[GH109]], [[GH177]], [[GH179]], and [[GH188]] has been shown to also require a NAD<sup>+</sup> cofactor.  The hydrolysis of thioglycosides with activated leaving groups has been documented in GH84 <cite>#23</cite>, GH1 <cite>#24 #25 #26 #27 #28 #29</cite>.  However, GH4 is currently the only family that has been shown to catalyze the hydrolysis of unactivated thioglycoside substrates <cite>#30</cite>.  The remarkable substrate specificities are all feasible due to the &beta;-elimination mechanism discussed below.
 ==Kinetics and Mechanism==

@@ Line 27: / Line 27: @@
 ==Substrate specificities==
-The majority of the [[glycoside hydrolases]] of this family are of bacterial origin, but they have recently been found in the archaeal taxa <cite>#1</cite>.  Unlike other families of glycosidases, some of the enzymes in Family 4 possess distinct substrate specificities from each other<cite>#1 #2</cite>.  This family contains &alpha;-glucosidases, &alpha;-galactosidases, &alpha;-glucuronidases, 6-phospho-&alpha;-glucosidases, and 6-phospho-&beta;-glucosidases.  Similar to [[GH1]], some enzymes prefer phosphorylated substrates over non-phosphorylated substrates <cite>#2 #3</cite>.  Unique to GH4 is the presence of both &alpha;- and &beta;-glycosidases.  The ability of a single enzyme to hydrolyze natural substrates of different anomeric configurations has not been discovered in other [[glycoside hydrolase]] families to-date.  GH4 enzymes were the first glycosidases shown to demonstrate an absolute requirement for NAD<sup>+</sup> and a divalent metal ion and in some instances reducing environments for catalytic activity <cite>#4 #5 #6 #7 #8 #9 #10 #11</cite>.  The cofactors are proposed to play key mechanistic roles in the atypical glycosidase mechanism.  Unlike GH4, metal ions are required by some glycosidases for structural integrity <cite>#12 #13</cite> or proper configuration of an active enzyme <cite>#14 #15 #16 #17</cite>.  Meanwhile, GH4 is the first family of glycoside hydrolases reported to require a NAD<sup>+</sup>  cofactor for catalytic activity <cite>#4 #5 #6 #7 #8 #10 #11 #18 #19 #20 #21 #22</cite>.  Subsequently, GH109 has more recently been shown to demonstrate the same use of a NAD<sup>+</sup> cofactor, but this family does not require metal ions or reducing conditions for activity.  The hydrolysis of thioglycosides with activated leaving groups has been documented in GH84 <cite>#23</cite>, GH1 <cite>#24 #25 #26 #27 #28 #29</cite>.  However, GH4 is currently the only family that has been shown to catalyze the hydrolysis of unactivated thioglycoside substrates <cite>#30</cite>.  The remarkable substrate specificities are all feasible due to the &beta;-elimination mechanism discussed below.
+The majority of the [[glycoside hydrolases]] of this family are of bacterial origin, but they have recently been found in the archaeal taxa <cite>#1</cite>.  Unlike other families of glycosidases, some of the enzymes in Family 4 possess distinct substrate specificities from each other<cite>#1 #2</cite>.  This family contains &alpha;-glucosidases, &alpha;-galactosidases, &alpha;-glucuronidases, 6-phospho-&alpha;-glucosidases, and 6-phospho-&beta;-glucosidases.  Similar to [[GH1]], some enzymes prefer phosphorylated substrates over non-phosphorylated substrates <cite>#2 #3</cite>.  Members of this family include both &alpha;- and &beta;-glycosidases.  The ability of a single enzyme to hydrolyze natural substrates of different anomeric configurations was first discovered in family GH4, and they were the first glycosidases that exhibited an absolute requirement for NAD<sup>+</sup> and a divalent metal ion and in some instances reducing environments for catalytic activity <cite>#4 #5 #6 #7 #8 #9 #10 #11</cite>.  The cofactors are proposed to play key mechanistic roles in the atypical glycosidase mechanism.  Unlike GH4, metal ions are required by some glycosidases for structural integrity <cite>#12 #13</cite> or proper configuration of an active enzyme <cite>#14 #15 #16 #17</cite>.  Meanwhile, GH4 is the first family of glycoside hydrolases reported to require a NAD<sup>+</sup>  cofactor for catalytic activity <cite>#4 #5 #6 #7 #8 #10 #11 #18 #19 #20 #21 #22</cite>.  Subsequently, enzymes of families [[GH109]], [[GH177]], [[GH179]], and [[GH188]] has been shown to also require a NAD<sup>+</sup> cofactor.  The hydrolysis of thioglycosides with activated leaving groups has been documented in GH84 <cite>#23</cite>, GH1 <cite>#24 #25 #26 #27 #28 #29</cite>.  However, GH4 is currently the only family that has been shown to catalyze the hydrolysis of unactivated thioglycoside substrates <cite>#30</cite>.  The remarkable substrate specificities are all feasible due to the &beta;-elimination mechanism discussed below.
 ==Kinetics and Mechanism==

@@ Line 15: / Line 15: @@
 |-
 |'''Mechanism'''
-|retaining
+|NAD-dependent hydrolysis
 |-
 |'''Active site residues'''

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Vivian Yip^^^
+* [[Author]]: [[User:Vivian Yip|Vivian Yip]]
-* [[Responsible Curator]]:  ^^^Steve Withers^^^
+* [[Responsible Curator]]:  [[User:Steve Withers|Steve Withers]]
 ----

@@ Line 89: / Line 89: @@
 #33 pmid=15237973
 #34 pmid=15341727
-#35 Koshland DE Jr: ''Stereochemistry and the mechanism of enzyme reactions.'' Biol Rev 1953, 28:416-436.
+#35 Koshland DE Jr: ''Stereochemistry and the mechanism of enzyme reactions.'' Biol Rev 1953, 28:416-436. [https://doi.org/10.1111/j.1469-185X.1953.tb01386.x DOI:10.1111/j.1469-185X.1953.tb01386.x]
 #36 pmid=16401086
 #37 pmid=10592235

@@ Line 22: / Line 22: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" | http://www.cazy.org/fam/GH4.html
+| colspan="2" | {{CAZyDBlink}}GH4.html
 |}
 </div>

@@ Line 27: / Line 27: @@
 ==Substrate specificities==
-The majority of the [[glycoside hydrolases]] of this family are of bacterial origin, but they have recently been found in the archaeal taxa <cite>#1</cite>.  Unlike other families of glycosidases, some of the enzymes in Family 4 possess distinct substrate specificities from each other<cite>#1 #2</cite>.  This family contains &alpha;-glucosidases, &alpha;-galactosidases, &alpha;-glucuronidases, 6-phospho-&alpha;-glucosidases, and 6-phospho-&beta;-glucosidases.  Similar to GH1, some enzymes prefer phosphorylated substrates over non-phosphorylated substrates <cite>#2 #3</cite>.  Unique to GH4 is the presence of both &alpha;- and &beta;-glycosidases.  The ability to hydrolyze natural substrates of different anomeric configurations has not been discovered in other glycoside hydrolase families to-date.  GH4 enzymes were the first glycosidases shown to demonstrate an absolute requirement for NAD<sup>+</sup> and a divalent metal ion and in some instances reducing environments for catalytic activity <cite>#4 #5 #6 #7 #8 #9 #10 #11</cite>.  The cofactors are proposed to play key mechanistic roles in the atypical glycosidase mechanism.  Unlike GH4, metal ions are required by some glycosidases for structural integrity <cite>#12 #13</cite> or proper configuration of an active enzyme <cite>#14 #15 #16 #17</cite>.  Meanwhile, GH4 is the first family of glycoside hydrolases reported to require a NAD<sup>+</sup>  cofactor for catalytic activity <cite>#4 #5 #6 #7 #8 #10 #11 #18 #19 #20 #21 #22</cite>.  Subsequently, GH109 has more recently been shown to demonstrate the same use of a NAD<sup>+</sup> cofactor, but this family does not require metal ions or reducing conditions for activity.  The hydrolysis of thioglycosides with activated leaving groups has been documented in GH84 <cite>#23</cite>, GH1 <cite>#24 #25 #26 #27 #28 #29</cite>.  However, GH4 is currently the only family that has been shown to catalyze the hydrolysis of unactivated thioglycoside substrates <cite>#30</cite>.  The remarkable substrate specificities are all feasible due to the &beta;-elimination mechanism discussed below.
+The majority of the [[glycoside hydrolases]] of this family are of bacterial origin, but they have recently been found in the archaeal taxa <cite>#1</cite>.  Unlike other families of glycosidases, some of the enzymes in Family 4 possess distinct substrate specificities from each other<cite>#1 #2</cite>.  This family contains &alpha;-glucosidases, &alpha;-galactosidases, &alpha;-glucuronidases, 6-phospho-&alpha;-glucosidases, and 6-phospho-&beta;-glucosidases.  Similar to [[GH1]], some enzymes prefer phosphorylated substrates over non-phosphorylated substrates <cite>#2 #3</cite>.  Unique to GH4 is the presence of both &alpha;- and &beta;-glycosidases.  The ability to hydrolyze natural substrates of different anomeric configurations has not been discovered in other glycoside hydrolase families to-date.  GH4 enzymes were the first glycosidases shown to demonstrate an absolute requirement for NAD<sup>+</sup> and a divalent metal ion and in some instances reducing environments for catalytic activity <cite>#4 #5 #6 #7 #8 #9 #10 #11</cite>.  The cofactors are proposed to play key mechanistic roles in the atypical glycosidase mechanism.  Unlike GH4, metal ions are required by some glycosidases for structural integrity <cite>#12 #13</cite> or proper configuration of an active enzyme <cite>#14 #15 #16 #17</cite>.  Meanwhile, GH4 is the first family of glycoside hydrolases reported to require a NAD<sup>+</sup>  cofactor for catalytic activity <cite>#4 #5 #6 #7 #8 #10 #11 #18 #19 #20 #21 #22</cite>.  Subsequently, GH109 has more recently been shown to demonstrate the same use of a NAD<sup>+</sup> cofactor, but this family does not require metal ions or reducing conditions for activity.  The hydrolysis of thioglycosides with activated leaving groups has been documented in GH84 <cite>#23</cite>, GH1 <cite>#24 #25 #26 #27 #28 #29</cite>.  However, GH4 is currently the only family that has been shown to catalyze the hydrolysis of unactivated thioglycoside substrates <cite>#30</cite>.  The remarkable substrate specificities are all feasible due to the &beta;-elimination mechanism discussed below.
 ==Kinetics and Mechanism==
@@ Line 35: / Line 35: @@
 ==Catalytic Residues==
-The proposed catalytic residues were mostly derived from x-ray crystallographic data and pH-dependent activity profiles obtained for BglT and GlvA <cite>#31 #32 #33 #36</cite>.  A Tyr residue that is conserved in all 6-phospho-&alpha;- and  6-phospho-&beta;-glycosidases was found to be approximately 4 &Aring; away from C2 of the reaction product, which can potentially act as a catalytic base <cite>#31 #32 #33 #34 #36</cite>.  The pH-dependent activity profiles were that of double ionization curves with pH<sub>opt</sub> at approximately 8 <cite>#32 #36</cite>.  Two p''K''<sub>a</sub> values of approximately 7 and 9 were determined <cite>#32 #36</cite>.  The p''K''<sub>a</sub> value of approximately 7 was proposed to correspond to that of the Tyr catalytic base, since this residue would need to be deprotonated for enzyme activity.  The position of the Tyr in the enzyme active site was used as a possible explanation for the relatively low p''K''<sub>a</sub> compared to that of a free Tyr (p''K''<sub>a</sub> = 10).  In the case of BglT, the Tyr residue is located at a distance of 3.4 &Aring; from the glycosidic oxygen, making it ideal to assume a second role in providing general acid catalysis to the departing oxygen as well as C2 deprotonation <cite>#31 #36</cite>.  The p''K''<sub>a</sub> value of approximately 9 was proposed to correspond to the ionization of the conserved Arg residue(s) that were found to be within hydrogen bonding distance of the phosphate group of the substrate in these two 6-phospho-glycosidases <cite>#31 #34 #36</cite>.  Again, the normal p''K''<sub>a</sub> of 12 for Arg could be lowered to 9, and this matches the expectation that protonated Arg residue(s) would be needed to form electrostatic interactions with the substrate phosphate moiety. Two other conserved residues, Cys and His, were shown to be responsible for chelating the metal ion in BglT and GlvA.  In the AglA structure, an Asp residue occupies the same position as the catalytic Tyr base, so the Asp is proposed to take on this role in AglA and possibly other GH4 enzymes that prefer non-phosphorylated substrates.
+The proposed catalytic residues were mostly derived from x-ray crystallographic data and pH-dependent activity profiles obtained for BglT and GlvA <cite>#31 #32 #33 #36</cite>.  A Tyr residue that is conserved in all 6-phospho-&alpha;- and  6-phospho-&beta;-glycosidases was found to be approximately 4 &Aring; away from C2 of the reaction product, which can potentially act as a [[general base]] <cite>#31 #32 #33 #34 #36</cite>.  The pH-dependent activity profiles were that of double ionization curves with pH<sub>opt</sub> at approximately 8 <cite>#32 #36</cite>.  Two p''K''<sub>a</sub> values of approximately 7 and 9 were determined <cite>#32 #36</cite>.  The p''K''<sub>a</sub> value of approximately 7 was proposed to correspond to that of the Tyr catalytic base, since this residue would need to be deprotonated for enzyme activity.  The position of the Tyr in the enzyme active site was used as a possible explanation for the relatively low p''K''<sub>a</sub> compared to that of a free Tyr (p''K''<sub>a</sub> = 10).  In the case of BglT, the Tyr residue is located at a distance of 3.4 &Aring; from the glycosidic oxygen, making it ideal to assume a second role in providing [[general acid]] catalysis to the departing oxygen as well as C2 deprotonation <cite>#31 #36</cite>.  The p''K''<sub>a</sub> value of approximately 9 was proposed to correspond to the ionization of the conserved Arg residue(s) that were found to be within hydrogen bonding distance of the phosphate group of the substrate in these two 6-phospho-glycosidases <cite>#31 #34 #36</cite>.  Again, the normal p''K''<sub>a</sub> of 12 for Arg could be lowered to 9, and this matches the expectation that protonated Arg residue(s) would be needed to form electrostatic interactions with the substrate phosphate moiety. Two other conserved residues, Cys and His, were shown to be responsible for chelating the metal ion in BglT and GlvA.  In the AglA structure, an Asp residue occupies the same position as the catalytic Tyr base, so the Asp is proposed to take on this role in AglA and possibly other GH4 enzymes that prefer non-phosphorylated substrates.
 ==Three-dimensional structures==

← Older revision		Revision as of 13:53, 8 November 2009
Line 1:		Line 1:
		+	{{CuratorApproved}}
	* [[Author]]: ^^^Vivian Yip^^^		* [[Author]]: ^^^Vivian Yip^^^
	* [[Responsible Curator]]: ^^^Steve Withers^^^		* [[Responsible Curator]]: ^^^Steve Withers^^^