PDBsum entry 2ber

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Hydrolase PDB id
Protein chain
601 a.a. *
Waters ×837
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Y370g active site mutant of the sialidase from micromonospora viridifaciens in complex with beta-neu5ac (sialic acid).
Structure: Bacterial sialidase. Chain: a. Fragment: residues 47-647. Synonym: neuraminidase. Engineered: yes. Mutation: yes
Source: Micromonospora viridifaciens. Organism_taxid: 1881. Atcc: 31146. Expressed in: escherichia coli. Expression_system_taxid: 469008.
1.80Å     R-factor:   0.143     R-free:   0.199
Authors: S.Newstead,J.N.Watson,A.J.Bennet,G.L.Taylor
Key ref:
S.Newstead et al. (2005). Structure and mechanism of action of an inverting mutant sialidase. Biochemistry, 44, 9117-9122. PubMed id: 15966735 DOI: 10.1021/bi050517t
30-Nov-04     Release date:   04-Apr-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q02834  (NANH_MICVI) -  Sialidase
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.  - 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: 10.1021/bi050517t Biochemistry 44:9117-9122 (2005)
PubMed id: 15966735  
Structure and mechanism of action of an inverting mutant sialidase.
S.Newstead, J.N.Watson, T.L.Knoll, A.J.Bennet, G.Taylor.
Mutagenesis of the conserved tyrosine (Y370) of the Micromonospora viridifaciens sialidase to small amino acids changes the mechanism of catalysis from retention of anomeric configuration to inversion [Watson, J. N., et al. (2003) Biochemistry 42, 12682-12690]. For the Y370G mutant enzyme-catalyzed hydrolysis of a series of aryl sialosides and 3'-sialyllactose, the derived Brønsted parameters (beta(lg)) on k(cat) and k(cat)/K(m) are -0.63 +/- 0.05 and -0.80 +/- 0.08, respectively. Thus, for the Y370G enzyme, glycosidic C-O bond cleavage is rate-determining. Analysis of the activity of the Y370G mutant and wild-type enzymes against a substrate [3,4-dihydro-2H-pyrano[3,2-c]pyridinium alpha-d-N-acetylneuraminide (DHP-alphaNeu5Ac)] whose hydrolysis cannot be accelerated by acid catalysis is consistent with these reactions proceeding via S(N)1 and S(N)2 mechanisms, respectively. The overall structure of the Y370G mutant sialidase active site is very similar to the previously reported wild-type structure [Gaskell, A., et al. (1995) Structure 3, 1197-1205], although removal of the tyrosine residue creates two significant changes to the active site. First, the anomeric oxygen atom of the hydrolysis product (beta-N-acetylneuraminic acid) and four water molecules bind in the large cavity created by the Y370G mutation. Second, the side chain of Asn310 moves to make a strong hydrogen bond to one of the bound water molecules.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20511247 A.Albohy, M.D.Li, R.B.Zheng, C.Zou, and C.W.Cairo (2010).
Insight into substrate recognition and catalysis by the human neuraminidase 3 (NEU3) through molecular modeling and site-directed mutagenesis.
  Glycobiology, 20, 1127-1138.  
19411257 T.J.Morley, L.M.Willis, C.Whitfield, W.W.Wakarchuk, and S.G.Withers (2009).
A new sialidase mechanism: bacteriophage K1F endo-sialidase is an inverting glycosidase.
  J Biol Chem, 284, 17404-17410.  
18625334 A.Buschiazzo, and P.M.Alzari (2008).
Structural insights into sialic acid enzymology.
  Curr Opin Chem Biol, 12, 565-572.  
16298994 A.G.Watts, P.Oppezzo, S.G.Withers, P.M.Alzari, and A.Buschiazzo (2006).
Structural and kinetic analysis of two covalent sialosyl-enzyme intermediates on Trypanosoma rangeli sialidase.
  J Biol Chem, 281, 4149-4155.
PDB codes: 2a75 2ags 2fhr
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.  
16495121 V.L.Yip, and S.G.Withers (2006).
Breakdown of oligosaccharides by the process of elimination.
  Curr Opin Chem Biol, 10, 147-155.  
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 codes are shown on the right.