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PDBsum entry 3b8s

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protein Protein-protein interface(s) links
Hydrolase PDB id
3b8s
Jmol
Contents
Protein chains
567 a.a. *
Waters ×1091
* Residue conservation analysis
PDB id:
3b8s
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
Resolution:
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
Date:
01-Nov-07     Release date:   01-Apr-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9AMP1  (Q9AMP1_VIBHA) -  Chitinase A
Seq:
Struc:
 
Seq:
Struc:
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.
 
  ABSTRACT  
 
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.  
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.