PDBsum entry: 3b9d

Hydrolase

PDB-id: 3b9d

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Description

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PROCHECK

Protein chain

567 a.a. *

Ligands

NAG-NAG-NAG-NAG

Waters ×664

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

3b9d

Name:

Hydrolase

Title:

Crystal structure of vibrio harveyi chitinase a complexed with pentasaccharide

Structure:

Chitinase a. Chain: a. Fragment: residues unp 22-597. Synonym: endochitinase a, glycosylhydrolase, family 18 chitinase. Engineered: yes. Mutation: 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

UniProt:

Q9AMP1 (Q9AMP1_VIBHA)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

850 a.a.

Struc:

567 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

1.72Å

R-factor:

0.188

R-free:

0.214

Authors:

C.Songsiriritthigul,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:

05-Nov-07

Release date:

01-Apr-08

Related entries:

3b8s
3b9a
3b9e

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Clefts

Surface

Key reference

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.