PDBsum entry 3b8s

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protein Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
567 a.a. *
Waters ×1091
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of wild-type chitinase a from vibrio harveyi
Structure: Chitinase a. Chain: a, b. Fragment: residues unp 22-597. Synonym: an endochitinase a, glycosylhydrolase, family 18 chitinase. Engineered: yes
Source: Vibrio harveyi. Organism_taxid: 669. Strain: lmg7890. Gene: chia. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: vibrio carchariae is synonym of vibrio harveyi
2.00Å     R-factor:   0.170     R-free:   0.205
Authors: C.Songsiriritthigul,S.Pantoom,A.H.Aguda,R.C.Robinson, W.Suginta
Key ref: C.Songsiriritthigul et al. (2008). Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism. J Struct Biol, 162, 491-499. PubMed id: 18467126 DOI: 10.1016/j.jsb.2008.03.008
01-Nov-07     Release date:   01-Apr-08    
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Protein chains
Pfam   ArchSchema ?
Q9AMP1  (Q9AMP1_VIBHA) -  Chitinase A
850 a.a.
567 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     2 terms  


DOI no: 10.1016/j.jsb.2008.03.008 J Struct Biol 162:491-499 (2008)
PubMed id: 18467126  
Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism.
C.Songsiriritthigul, S.Pantoom, A.H.Aguda, R.C.Robinson, W.Suginta.
This research describes four X-ray structures of Vibrio harveyi chitinase A and its catalytically inactive mutant (E315M) in the presence and absence of substrates. The overall structure of chitinase A is that of a typical family-18 glycosyl hydrolase comprising three distinct domains: (i) the amino-terminal chitin-binding domain; (ii) the main catalytic (alpha/beta)(8) TIM-barrel domain; and (iii) the small (alpha+beta) insertion domain. The catalytic cleft of chitinase A has a long, deep groove, which contains six chitooligosaccharide ring-binding subsites (-4)(-3)(-2)(-1)(+1)(+2). The binding cleft of the ligand-free E315M is partially blocked by the C-terminal (His)(6)-tag. Structures of E315M-chitooligosaccharide complexes display a linear conformation of pentaNAG, but a bent conformation of hexaNAG. Analysis of the final 2F(o)-F(c) omit map of E315M-NAG6 reveals the existence of the linear conformation of the hexaNAG at a lower occupancy with respect to the bent conformation. These crystallographic data provide evidence that the interacting sugars undergo conformational changes prior to hydrolysis by the wild-type enzyme.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21240541 T.Ohnuma, T.Numata, T.Osawa, M.Mizuhara, K.M.Vårum, and T.Fukamizo (2011).
Crystal structure and mode of action of a class V chitinase from Nicotiana tabacum.
  Plant Mol Biol, 75, 291-304.
PDB codes: 3alf 3alg
20714419 F.Khoushab, and M.Yamabhai (2010).
Chitin research revisited.
  Mar Drugs, 8, 1988-2012.  
20084296 H.Li, and L.H.Greene (2010).
Sequence and structural analysis of the chitinase insertion domain reveals two conserved motifs involved in chitin-binding.
  PLoS One, 5, e8654.  
19568782 W.Suginta, S.Pantoom, and H.Prinz (2009).
Substrate binding modes and anomer selectivity of chitinase A from Vibrio harveyi.
  J Chem Biol, 2, 191-202.  
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