Glycoside Hydrolase Family 58 - Revision history

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

2021-12-18T21:19:09Z

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

2012-09-10T16:40:01Z

updated CAZyDBlink

2011-06-14T03:12:19Z

2010-02-15T07:40:50Z

Three-dimensional structures

2010-01-22T14:40:59Z

Three-dimensional structures

2010-01-18T17:47:09Z

2010-01-18T17:44:54Z

2010-01-14T08:47:56Z

Family Firsts

2010-01-14T08:45:10Z

Three-dimensional structures

2010-01-14T08:43:28Z

Catalytic Residues

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 <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
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-* [[Author]]: ^^^Warren Wakarchuk^^^
+* [[Author]]: [[User:Warren Wakarchuk|Warren Wakarchuk]]
-* [[Responsible Curator]]:  ^^^Warren Wakarchuk^^^
+* [[Responsible Curator]]:  [[User:Warren Wakarchuk|Warren Wakarchuk]]
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 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH58.html
+| colspan="2" |{{CAZyDBlink}}GH58.html
 |}
 </div>

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 == Substrate specificities ==
-[[Glycoside hydrolases]] of family 58 are [[endo]]-''N''-acetylneuraminidases (also termed [[endo]]-sialidases). The capsular coat surrounding ''E. coli'' K1, is poly-alpha-2,8-sialic acid and protects the bacterium from the host immune system, but it also acts as an anchor point for bacteriophage infection.  A range of bacteriophages specific to this ''E. coli'' capsule type have been described which have tailspike enzymes that degrade the capuslar material <cite>Kwiatowski Hallenbeck Petter</cite>
+[[Glycoside hydrolases]] of family 58 are [[endo]]-''N''-acetylneuraminidases (also termed [[endo]]-sialidases). The capsular coat surrounding ''E. coli'' K1, is poly-&alpha;-2,8-sialic acid and protects the bacterium from the host immune system, but it also acts as an anchor point for bacteriophage infection.  A range of bacteriophages specific to this ''E. coli'' capsule type have been described which have tailspike enzymes that degrade the capuslar material <cite>Kwiatowski Hallenbeck Petter</cite>
 == Kinetics and Mechanism ==

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 The structure for the K1F tailspike enzyme has been solved by Stummeyer et al. <cite>Stummeyer</cite>.  The protein structure is similar to other phage tailspike endo-hydrolases in that it is an extended, trimeric molecule.  The first tailspike enzyme to be studied in detail was the endo-rhamnosidase from the Salmonella phage P22 <cite>Steinbacher</cite>, which is in family [[GH90]].  The pictures here were generated in [http://www.pymol.org/ Pymol] from PDB entry [{{PDBlink}}1voe 1voe].  Each monomer is a different colour to highlight the trimeric nature of the protein.
-<gallery widths=320px heights=240px perrow=2 caption="Top and side views of PDB ID 1voe from GH58 (click images for large versions)">
+<gallery widths=320px heights=240px perrow=2 caption="PDB ID 1voe from GH58 (click images for large versions)">
-File:Gh581.png
+File:Gh581.png|top view
-File:Gh58_2.png
+File:Gh58_2.png|side view
 </gallery>

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 == Three-dimensional structures ==
 The structure for the K1F tailspike enzyme has been solved by Stummeyer et al. <cite>Stummeyer</cite>.  The protein structure is similar to other phage tailspike endo-hydrolases in that it is an extended, trimeric molecule.  The first tailspike enzyme to be studied in detail was the endo-rhamnosidase from the Salmonella phage P22 <cite>Steinbacher</cite>, which is in family [[GH90]].  The pictures here were generated in [http://www.pymol.org/ Pymol] from PDB entry [{{PDBlink}}1voe 1voe].  Each monomer is a different colour to highlight the trimeric nature of the protein.
-[[Image:Gh581.png|left|thumb|300 px|[{{PDBlink}}1voe 1voe], top view, GH58]]
-[[Image:Gh58_2.png|right|thumb|300 px|[{{PDBlink}}1voe 1voe], side view, GH58]]
+<gallery widths=320px heights=240px perrow=2 caption="Top and side views of PDB ID 1voe from GH58 (click images for large versions)">
-<br style="clear: both" />
+File:Gh581.png
 == Family Firsts ==

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 |-
 |'''Active site residues'''
-|not known
+|Arg596, Arg647 and Glu581
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''

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 ;First sterochemistry determination: The stereochemical outcome of this reaction was determined in the Withers laboratory at UBC using synthetic substrates with a trifluoromethyl-umbelliferol fluorophore <cite>Morely</cite>.  This determination showed that unlike all other known sialidases, the [[endo]]-sialidase uses an [[inverting]] mechanism.
 ;First [[catalytic nucleophile]] identification: Since this enzyme proceeds with inversion of sterechemistry, is does not use a catalytic nuceleophile.
-;First [[general acid/base]] residue identification:
+;First [[general acid/base]] residue identification: It has been suggested though not conclusively proven that Glu581 is the catalytic base for this reaction <cite>Stummeyer Morely</cite>.
 ;First 3-D structure: The first structure determination was performed with a truncated version of the K1F protein <cite>Stummeyer</cite>.

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 == Catalytic Residues ==
-From the crystal structure of the GH-58 enzyme it was noted that the normal catalyic residues found in exo-sialidases were not present.  Instead, three conserved amino acids (Arg596,Arg647 and Glu581) were observed that contribute to endosialidase activity.  Single mutations of those residues reduced the level of activity, but not enough to mark the residues as absolutely required.  However, when double mutants were examined there was a complete loss of hydrolysis, but binding to PSA still occured <cite>Stummeyer</cite>.  Since this enzyme proceeds with inverting stereochemistry, a catalytic base is implied by the mechanism, and Glu581 might fill that role <cite>Morely</cite>.
+From the crystal structure of the GH-58 enzyme it was noted that the normal catalyic residues found in exo-sialidases were not present.  Instead, three conserved amino acids (Arg596, Arg647 and Glu581) were observed that contribute to endosialidase activity.  Single mutations of those residues reduced the level of activity, but not enough to mark the residues as absolutely required.  However, when double mutants were examined there was a complete loss of hydrolysis, but binding to PSA still occured <cite>Stummeyer</cite>.  Since this enzyme proceeds with inverting stereochemistry, a catalytic base is implied by the mechanism, and Glu581 might fill that role <cite>Morely</cite>.
 == Three-dimensional structures ==