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PDBsum entry 1w8o

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protein ligands metals links
Hydrolase PDB id
1w8o
Jmol
Contents
Protein chain
601 a.a. *
Ligands
LBT
CIT
GOL ×4
Metals
_NA
Waters ×709
* Residue conservation analysis
PDB id:
1w8o
Name: Hydrolase
Title: Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from micromonospora viridifaciens
Structure: Bacterial sialidase. Chain: a. Fragment: residues 47-647. Engineered: yes. Mutation: yes
Source: Micromonospora viridifaciens. Organism_taxid: 1881. Atcc: 31146. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.70Å     R-factor:   0.164     R-free:   0.197
Authors: S.Newstead,J.N.Watson,V.Dookhun,A.J.Bennet,G.Taylor
Key ref:
J.N.Watson et al. (2004). Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from Micromonospora viridifaciens. FEBS Lett, 577, 265-269. PubMed id: 15527797 DOI: 10.1016/j.febslet.2004.10.016
Date:
24-Sep-04     Release date:   29-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q02834  (NANH_MICVI) -  Sialidase
Seq:
Struc:
 
Seq:
Struc:
647 a.a.
601 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.18  - Exo-alpha-sialidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     exo-alpha-(2->3)-sialidase activity     6 terms  

 

 
DOI no: 10.1016/j.febslet.2004.10.016 FEBS Lett 577:265-269 (2004)
PubMed id: 15527797  
 
 
Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from Micromonospora viridifaciens.
J.N.Watson, S.Newstead, V.Dookhun, G.Taylor, A.J.Bennet.
 
  ABSTRACT  
 
A recombinant D92G mutant sialidase from Micromonospora viridifaciens has been cloned, expressed and purified. Kinetic studies reveal that the replacement of the conserved aspartic acid with glycine results in a catalytically competent retaining sialidase that possesses significant activity against activated substrates. The contribution of this aspartate residue to the free energy of hydrolysis for natural substrates is greater than 19 kJ/mol. The three dimensional structure of the D92G mutant shows that the removal of aspartic acid 92 causes no significant re-arrangement of the active site, and that an ordered water molecule substitutes for the carboxylate group of D92.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Effect of temperature on the relative rates of sialidase-catalyzed hydrolysis of MU-αNeu5Ac at pH 5.25 for the wild-type enzyme ( operator ) and D92G mutant (•). Data for wild-type reproduced with permission of the American Chemical Society.
Figure 5.
Fig. 5. Superimposition of the active site residues of wild-type catalytic domain with Neu5Ac2en (PDB 1EUS) and the D92G-Neu5Ac2en complex. Residues of the wild-type structure are shown in slate and of the mutant in wheat. The hydrogen bonding interactions are drawn as green dotted lines; the interaction of Asp92 with Asp85 is shown in orange.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2004, 577, 265-269) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20939100 S.Kalkhof, S.Haehn, M.Paulsson, N.Smyth, J.Meiler, and A.Sinz (2010).
Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking.
  Proteins, 78, 3409-3427.  
17268638 D.Indurugalla, J.N.Watson, and A.J.Bennet (2006).
Natural sialoside analogues for the determination of enzymatic rate constants.
  Org Biomol Chem, 4, 4453-4459.  
16206228 J.N.Watson, S.Newstead, A.A.Narine, G.Taylor, and A.J.Bennet (2005).
Two nucleophilic mutants of the Micromonospora viridifaciens sialidase operate with retention of configuration by two different mechanisms.
  Chembiochem, 6, 1999-2004.
PDB code: 1wcq
15864320 J.N.Watson, T.L.Knoll, J.H.Chen, D.T.Chou, T.J.Borgford, and A.J.Bennet (2005).
Use of conformationally restricted pyridinium alpha-D-N-acetylneuraminides to probe specificity in bacterial and viral sialidases.
  Biochem Cell Biol, 83, 115-122.  
16239725 S.L.Newstead, J.N.Watson, A.J.Bennet, and G.Taylor (2005).
Galactose recognition by the carbohydrate-binding module of a bacterial sialidase.
  Acta Crystallogr D Biol Crystallogr, 61, 1483-1491.
PDB codes: 2bq9 2bzd
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.