Glycoside Hydrolase Family 88 - Revision history

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

2021-12-18T21:18:57Z

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

Harry Brumer: added DOI for Koshland ref.

2019-07-17T17:29:56Z

added DOI for Koshland ref.

Harry Brumer: upgraded to Curator Approved status

2019-07-17T17:29:11Z

upgraded to Curator Approved status

Harry Brumer at 16:12, 24 June 2019

2019-06-24T16:12:04Z

Harry Brumer at 16:11, 24 June 2019

2019-06-24T16:11:36Z

Harry Brumer at 16:08, 24 June 2019

2019-06-24T16:08:48Z

Harry Brumer: added italics to species names

2019-06-24T16:08:26Z

added italics to species names

Harry Brumer: added GH105 link

2019-06-24T16:06:32Z

added GH105 link

Harry Brumer: adjusted punctuation and paragraph spacing

2015-10-19T14:36:04Z

adjusted punctuation and paragraph spacing

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Seino Jongkees at 06:24, 17 October 2015

2015-10-17T06:24:26Z

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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]]: ^^^Seino Jongkees^^^
+* [[Author]]: [[User:Seino Jongkees|Seino Jongkees]]
-* [[Responsible Curator]]:  ^^^Steve Withers^^^
+* [[Responsible Curator]]:  [[User:Steve Withers|Steve Withers]]
 ----

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 #Yip2006 pmid=16917793
 #Jongkees2014b pmid=24573682
-#Koshland1953 Koshland DE Jr: ''Stereochemistry and the mechanism of enzyme reactions.'' Biol Rev 1953, 28:416-436.
+#Koshland1953 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]
 #Itoh2004 pmid=15148314
 #Itoh2006b pmid=16630576

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: ^^^Seino Jongkees^^^
 * [[Responsible Curator]]:  ^^^Steve Withers^^^

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 == Catalytic Residues ==
-Catalytic residues have been proposed based on sequence conservation, x-ray crystallography, and site-directed mutagenesis studies <cite>Itoh2006a Itoh2004</cite>. These amino acids, a pair of aspartate or glutamate residues, were initially thought to be involved in an inverting type mechanism, on the basis of their separation distance <cite>Itoh2004</cite>. Subsequent solving of x-ray crystal structures of a catalytically-inactive mutant with substrates bound led to the proposal of the hydration-initiated mechanism outlined above <cite>Itoh2006a</cite>. However, while two carboxylate-containing residues are present in the active site, and mutation of either to the corresponding amide side-chain gives a mutant with near-negligible activity, only one of these has a clear role. Aspartate number 149 in ''Bacillus'' sp. GL1 UGL is situated 2.9 Å from the substrate carbon 4, and plays the role of a catalytic acid to protonate the C4-C5 double bond in the substrate, thereby initiating hydration. Aspartate 88 in the same enzyme, as the asparagine mutant, is situated adjacent to the hydroxyl groups on carbons 2 and 3, at around 2.4 Å from each. This residue has no proposed role in a direct hydration mechanism that could account for its apparent importance in catalysis. However, it has been proposed that this residue may be important for the formation of a transient intermediate in the hydration step <cite>Jongkees2014b</cite>.
+Catalytic residues have been proposed based on sequence conservation, X-ray crystallography, and site-directed mutagenesis studies <cite>Itoh2006a Itoh2004</cite>. These amino acids, a pair of aspartate or glutamate residues, were initially thought to be involved in an inverting type mechanism, on the basis of their separation distance <cite>Itoh2004</cite>. Subsequent solving of x-ray crystal structures of a catalytically-inactive mutant with substrates bound led to the proposal of the hydration-initiated mechanism outlined above <cite>Itoh2006a</cite>. However, while two carboxylate-containing residues are present in the active site, and mutation of either to the corresponding amide side-chain gives a mutant with near-negligible activity, only one of these has a clear role. Aspartate number 149 in ''Bacillus'' sp. GL1 UGL is situated 2.9 Å from the substrate carbon 4, and plays the role of a catalytic acid to protonate the C4-C5 double bond in the substrate, thereby initiating hydration. Aspartate 88 in the same enzyme, as the asparagine mutant, is situated adjacent to the hydroxyl groups on carbons 2 and 3, at around 2.4 Å from each. This residue has no proposed role in a direct hydration mechanism that could account for its apparent importance in catalysis. However, it has been proposed that this residue may be important for the formation of a transient intermediate in the hydration step <cite>Jongkees2014b</cite>.
 == Three-dimensional structures ==

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 == Substrate specificities ==
-GH88 enzymes are unsaturated glucuronyl hydrolases, and are predominantly found expressed in bacteria, although a small number have been annotated in archaea and fungi <cite>Cantarel2009</cite>. These enzymes are atypical in that they hydrolyse their substrates through hydration of a double bond between carbons 4 and 5 of the non-reducing terminal sugar of their substrates <cite>Itoh2006a Jongkees2011</cite>. Substrates for GH88 are derived for the most part from the activity of polysaccharide lyases on glycosaminoglycans, and so are &beta;-1,3- or &beta;-1,4-linked (before elimination; lyase cleavage changes the reference stereocenter, leading to the products being &alpha; linked, but the anomeric bond does not change). The preferred pattern of sulphation in substrates varies with the source organism <cite>Hashimoto1999 Myette2002 Mori2003 Maruyama2009 Nakamichi2011 Marion2012 Nakamichi2014 Jongkees2014a</cite>, and a flexible loop adjacent to the +2 subsite has been identified as an important determinant of this preference <cite>Nakamichi2011</cite>. The related family [[GH105]] contains enzymes that cleave alpha linked substrates, typically working on substrates derived from rhamnogalacturonans <cite>Itoh2006a Itoh2006b</cite>. Aside from glycosaminoglycans, unsaturated uronic acid-containing oligosaccharides from gellan and xanthan have also been identified as substrates <cite>Hashimoto1999 Mori2003</cite>.
+GH88 enzymes are unsaturated glucuronyl hydrolases, and are predominantly found expressed in bacteria, although a small number have been annotated in archaea and fungi <cite>Cantarel2009</cite>. These enzymes are atypical in that they hydrolyse their substrates through hydration of a double bond between carbons 4 and 5 of the non-reducing terminal sugar of their substrates <cite>Itoh2006a Jongkees2011</cite>. Substrates for GH88 are derived for the most part from the activity of [[Polysaccharide Lyases]] on glycosaminoglycans, and so are &beta;-1,3- or &beta;-1,4-linked (before elimination; lyase cleavage changes the reference stereocenter, leading to the products being &alpha; linked, but the anomeric bond does not change). The preferred pattern of sulphation in substrates varies with the source organism <cite>Hashimoto1999 Myette2002 Mori2003 Maruyama2009 Nakamichi2011 Marion2012 Nakamichi2014 Jongkees2014a</cite>, and a flexible loop adjacent to the +2 subsite has been identified as an important determinant of this preference <cite>Nakamichi2011</cite>. The related family [[GH105]] contains enzymes that cleave alpha linked substrates, typically working on substrates derived from rhamnogalacturonans <cite>Itoh2006a Itoh2006b</cite>. Aside from glycosaminoglycans, unsaturated uronic acid-containing oligosaccharides from gellan and xanthan have also been identified as substrates <cite>Hashimoto1999 Mori2003</cite>.
 GH88 from ''Clostridium perfringens'' has also been shown to be capable of acting on several unusual substrates <cite>Jongkees2011</cite>. It is able to hydrate a C-glycosidic substrate analogue, and hydrolyses both the thioglycoside analogue and the alternate anomer of phenyl unsaturated glucuronic acid. Previously, only [[GH84]] <cite>Macauley2005</cite>, [[GH1]] <cite>Day1986 Burmeister1997 Burmeister2000 Cottaz1996 McDanell1988 Xue1992</cite>, and [[GH4]] <cite>Yip2006</cite> had been shown to hydrolyse thioglycosides. UGL is able to hydrolyse a range of synthetic substrates with aromatic leaving groups, as well as unsaturated glucuronyl fluoride with both anomeric stereochemistries <cite>Jongkees2014a</cite>, with k<sub>cat</sub> decreasing as electron withdrawing ability increases. Finally, substrates with the hydroxyl group on carbon 2 replaced appear to be turned over very poorly <cite>Myette2002 Jongkees2014b Jongkees2014a</cite>, although in some cases sulfation appears to at least be partially tolerated in this position <cite>Hashimoto1999 Mori2003 Maruyama2009 Nakamichi2014</cite>.
 == Kinetics and Mechanism ==
-The GH88 family enzymes do not follow a classical Koshland inverting or retaining mechanism <cite>Koshland1953</cite>. Enzymes in this family instead are believed to trigger hydrolysis by hydration of the double bond between carbons 4 and 5 in their substrates. This hydration product, a hemiketal, then undergoes a series of rearrangements &mdash; forming first an intermediate hemiacetal, then loss of the anomeric substituent to give an open chain product, which can then be hydrated in water. This mechanism was initially proposed based on catalytic residue placement in a substrate-bound crystal structure <cite>Itoh2006a</cite>, and subsequently confirmed by kinetic isotope effect and NMR data <cite>Jongkees2011</cite>. The initial hydration is a syn addition of water to the double bond, while carbon 1 cannot be said to have a stereochemical outcome, as it is an aldehyde in the first-formed product and immediately forms a mixture of anomers <cite>Jongkees2011</cite>. The rearrangements from hemiketal to open chain product have been suggested to be catalysed by the enzyme on the basis of NMR studies looking for the first detectable products under high enzyme concentration conditions, wherein no intermediates were seen to accumulate in solution <cite>Jongkees2014b</cite>.
+The GH88 family enzymes do not follow a classical Koshland [[inverting mechanism]] or [[retaining mechanism]] <cite>Koshland1953</cite>. Enzymes in this family instead are believed to trigger hydrolysis by hydration of the double bond between carbons 4 and 5 in their substrates. This hydration product, a hemiketal, then undergoes a series of rearrangements &mdash; forming first an intermediate hemiacetal, then loss of the anomeric substituent to give an open chain product, which can then be hydrated in water. This mechanism was initially proposed based on catalytic residue placement in a substrate-bound crystal structure <cite>Itoh2006a</cite>, and subsequently confirmed by kinetic isotope effect and NMR data <cite>Jongkees2011</cite>. The initial hydration is a syn addition of water to the double bond, while carbon 1 cannot be said to have a stereochemical outcome, as it is an aldehyde in the first-formed product and immediately forms a mixture of anomers <cite>Jongkees2011</cite>. The rearrangements from hemiketal to open chain product have been suggested to be catalysed by the enzyme on the basis of NMR studies looking for the first detectable products under high enzyme concentration conditions, wherein no intermediates were seen to accumulate in solution <cite>Jongkees2014b</cite>.
 Based on kinetic data, the hydration step of the mechanism appears to proceed through a short-lived intermediate. This intermediate has been suggested to be a pyranose-ring-opened structure with a C4 ketone and a C1-C2 epoxide, on the basis of kinetic isotope effects, C2 hydroxyl group substitutions, and catalytic residue placement <cite>Jongkees2014b</cite>. However, there is not yet any direct evidence for this. The overall rate-limiting step of this mechanism is believed to be the breakdown of this intermediate of the hydration process, on the basis of kinetic isotope effects <cite>Jongkees2014b</cite> and consistent with LFER data <cite>Jongkees2014a</cite>.

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 ;First stereochemistry determination
 :''Bacillus'' sp. GL1 UGL (unsaturated glucuronyl hydrolase), enzyme alone <cite>Itoh2004</cite>
-:''Bacillus sp.'' GL1 UGL (unsaturated glucuronyl hydrolase), substrate bound <cite>Itoh2006a</cite>
+:''Bacillus'' sp. GL1 UGL (unsaturated glucuronyl hydrolase), substrate bound <cite>Itoh2006a</cite>
 ;First catalytic residue determination
 :''Bacillus'' sp. GL1 UGL (unsaturated glucuronyl hydrolase),  via x-ray crystal structure <cite>Itoh2004</cite>

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 == Family Firsts ==
 ;First stereochemistry determination
-:Bacillus sp. GL1 UGL (unsaturated glucuronyl hydrolase), enzyme alone <cite>Itoh2004</cite>
+:''Bacillus'' sp. GL1 UGL (unsaturated glucuronyl hydrolase), enzyme alone <cite>Itoh2004</cite>
-:Bacillus sp. GL1 UGL (unsaturated glucuronyl hydrolase), substrate bound <cite>Itoh2006a</cite>
+:''Bacillus sp.'' GL1 UGL (unsaturated glucuronyl hydrolase), substrate bound <cite>Itoh2006a</cite>
 ;First catalytic residue determination
-:Bacillus sp. GL1 UGL (unsaturated glucuronyl hydrolase),  via x-ray crystal structure <cite>Itoh2004</cite>
+:''Bacillus'' sp. GL1 UGL (unsaturated glucuronyl hydrolase),  via x-ray crystal structure <cite>Itoh2004</cite>
 ;First stereochemistry determination (hydration)
-:Clostridium perfringens UGL (unsaturated glucuronyl hydrolase),  via NMR of methyl ketal intermediate analogue and product of reaction in deuterated water <cite>Jongkees2011</cite>
+:''Clostridium perfringens'' UGL (unsaturated glucuronyl hydrolase),  via NMR of methyl ketal intermediate analogue and product of reaction in deuterated water <cite>Jongkees2011</cite>
 ;First evidence for intermediate in hydration
-:Clostridium perfringens UGL (unsaturated glucuronyl hydrolase),  from kinetic isotope effects and substrate analogues <cite>Jongkees2014b</cite>
+:''Clostridium perfringens'' UGL (unsaturated glucuronyl hydrolase),  from kinetic isotope effects and substrate analogues <cite>Jongkees2014b</cite>
 == References ==