Difference between revisions of "Glycoside Hydrolase Family 58"

Revision as of 05:37, 26 October 2009

This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.

Author: ^^^Warren Wakarchuk^^^
Responsible Curator: ^^^Warren Wakarchuk^^^

Glycoside Hydrolase Family GH58
Clan	none
Mechanism	inverting
Active site residues	not known
CAZy DB link
http://www.cazy.org/fam/GH58.html

Substrate specificities

Glycoside hydrolases of family 58 are endo-N-acetylneuraminidases (also termed endo-sialidases). The capsular coat surrounding E. coli K1, protects the bacterium from degradation by the host immune system, but it also acts as an anchor point for bacteriophage infection. The capsular material for K1 is poly-alpha-2,8-sialic acid and a range of bacteriophages specific to this E. coli capsule type have been described which have tailspike enzymes that degrade the capuslar material [1, 2, 3]

Kinetics and Mechanism

Fanily 58 endo-sialidases are specific for polysialic acid and form a unique family of endo-acting sialidases, all others previously reported being exo-acting. The recently determined structure of an endo-sialidase derived from bacteriophage K1F (endoNF)[3] revealed the active site to lack a number of the residues that are conserved in other sialidases, implying a new, endo-sialidase-specific catalytic mechanism. Using synthetic trifluoromethylumbelliferyl oligosialoside substrates kinetic parameters for hydrolysis at a single cleavage site were determined. Measurement of k_cat/K_m at a series of pH values revealed a dependence on a single protonated group of pK_a 5. Direct ¹H-NMR analysis of the hydrolysis of trifluoromethylumbelliferyl sialotrioside revealed that endoNF undergoes catalysis with and inverting mechanism [4, 5, 6, 7].

Catalytic Residues

Content is to be added here.

Three-dimensional structures

The structure for the K1F tailspike enzyme has been solved by Stummeyer et al. [8]. The protein structure is similar to other phage tailspike endo-hydrolases in that it is a an extended molecule that is trimeric.

Can you cross-reference other GH families in CAzypedia here? Harry Brumer 16:17, 23 October 2009 (UTC)

Family Firsts

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 [4, 5, 6, 7]. This determination showed that unlike all other known sialidases, the endo-sialidase uses an inverting mechanism.
First catalytic nucleophile identification: Cite some reference here, with a short (1-2 sentence) explanation .
First general acid/base residue identification: Cite some reference here, with a short (1-2 sentence) explanation .
First 3-D structure: The first structure determination was performed with the K1F protein [5, 6, 9].

References

All Medline abstracts: PubMed

@@ Line 18: / Line 18: @@
 |-
 |'''Active site residues'''
-|known/not known
+|not known
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
@@ Line 32: / Line 32: @@
 == Kinetics and Mechanism ==
-Fanily 58 [[endo]]-sialidases are specific for polysialic acid and form a unique family of [[endo]]-acting sialidases, all others previously reported being [[exo]]-acting. The recently determined structure of an [[endo]]-sialidase derived from bacteriophage K1F (endoNF)<cite>3</cite> revealed the active site to lack a number of the residues that are conserved in other sialidases, implying a new, [[endo]]-sialidase-specific catalytic mechanism. Using synthetic trifluoromethylumbelliferyl oligosialoside substrates kinetic parameters for hydrolysis at a single cleavage site were determined. Measurement of ''k<sub>cat</sub>/K<sub>m</sub>'' at a series of pH values revealed a dependence on a single protonated group of pK<sub>a</sub> 5. Direct <sup>1</sup>H-NMR analysis of the hydrolysis of trifluoromethylumbelliferyl sialotrioside revealed that endoNF undergoes catalysis with and [[inverting]] mechanism <cite>4</cite>.
+Fanily 58 [[endo]]-sialidases are specific for polysialic acid and form a unique family of [[endo]]-acting sialidases, all others previously reported being [[exo]]-acting. The recently determined structure of an [[endo]]-sialidase derived from bacteriophage K1F (endoNF)<cite>3</cite> revealed the active site to lack a number of the residues that are conserved in other sialidases, implying a new, [[endo]]-sialidase-specific catalytic mechanism. Using synthetic trifluoromethylumbelliferyl oligosialoside substrates kinetic parameters for hydrolysis at a single cleavage site were determined. Measurement of ''k<sub>cat</sub>/K<sub>m</sub>'' at a series of pH values revealed a dependence on a single protonated group of pK<sub>a</sub> 5. Direct <sup>1</sup>H-NMR analysis of the hydrolysis of trifluoromethylumbelliferyl sialotrioside revealed that endoNF undergoes catalysis with and [[inverting]] mechanism <cite>Morely et al 2009</cite>.
 == Catalytic Residues ==
@@ Line 44: / Line 44: @@
 == Family Firsts ==
-;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>3</cite>.  This determination showed that unlike all other known sialidases, the [[endo]]-sialidase uses an [[inverting]] mechanism.
+;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 et al 2009</cite>.  This determination showed that unlike all other known sialidases, the [[endo]]-sialidase uses an [[inverting]] mechanism.
-;First [[catalytic nucleophile]] identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>MikesClassic</cite>.
+;First [[catalytic nucleophile]] identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation .
-;First [[general acid/base]] residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.
+;First [[general acid/base]] residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation .
-;First 3-D structure: The first structure determination was performed with the K1F protein <cite>3</cite>.
+;First 3-D structure: The first structure determination was performed with the K1F protein <cite>Strummer et al</cite>.
 == References ==