PDBsum entry: 1v5d

Hydrolase

PDB-id: 1v5d

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

386 a.a. *

Ligands

PIN

Waters ×1003

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1v5d

Name:

Hydrolase

Title:

The crystal structure of the active form chitosanase from bacillus sp. K17 at ph6.4

Structure:

Chitosanase. Chain: a, b. Ec: 3.2.1.132

Source:

Bacillus sp.. Organism_taxid: 1409. Strain: k17

UniProt:

Chains A, B: Q9ALZ1 (Q9ALZ1_9BACI)

Seq:

Struc:

Seq:

453 a.a.

Struc:

386 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Resolution:

1.50Å

R-factor:

0.167

R-free:

0.189

Authors:

W.Adachi,S.Shimizu,T.Sunami,T.Fukazawa,M.Suzuki,R.Yatsunami, S.Nakamura,A.Takenaka

Key ref:

W.Adachi et al. (2004). Crystal structure of family GH-8 chitosanase with subclass II specificity from Bacillus sp. K17.. J Mol Biol, 343, 785-795. [PubMed id: 15465062] [DOI: 10.1016/j.jmb.2004.08.028]

Date:

22-Nov-03

Release date:

07-Dec-04

Related entries:

1v5c
the same protein, the inactive form at ph3.7

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/j.jmb.2004.08.028

J Mol Biol 343:785-795 (2004)

PubMed id: 15465062

Crystal structure of family GH-8 chitosanase with subclass II specificity from Bacillus sp. K17.

W.Adachi, Y.Sakihama, S.Shimizu, T.Sunami, T.Fukazawa, M.Suzuki, R.Yatsunami, S.Nakamura, A.Takénaka.

ABSTRACT

Crystal structures of chitosanase from Bacillus sp. K17 (ChoK) have been determined at 1.5 A resolution in the active form and at 2.0 A resolution in the inactive form. This enzyme belongs to the family GH-8, out of 93 glycoside hydrolase families, and exhibits the substrate specificity of subclass II chitosanase. The catalytic site is constructed on the scaffold of a double-alpha(6)/alpha(6)-barrel, which is formed by six repeating helix-loop-helix motifs. This structure is quite different from those of the GH-46 chitosanases and of GH-5. Structural comparison with CelA (a cellulase belonging to the same family GH-8) suggests that the proton donor Glu122 is conserved, but the proton acceptor is the inserted Glu309 residue, and that the corresponding Asp278 residue in CelA is inactivated in ChoK. The four acidic residues, Asp179, Glu309, Asp183 and Glu107, can be involved in substrate recognition through interactions with the amino groups of the glucosamine residues bound in the -3, -2, -1 and +1 sites, respectively. The hydrophobic Trp235, Trp166, Phe413 and Tyr318 residues are highly conserved for binding of the hexose rings at the -3, -2, +1 and +2 sites, respectively. These structural features indicate that enzymes in GH-8 can be further divided into three subfamilies. Different types of chitosanases are discussed in terms of convergent evolution from different structural ancestors.

Selected figure(s)

Figure 3.
Figure 3. Stereo-pair diagrams of the active form of ChoK. In (a) the top view and (b) the side view, the two catalytic residues Glu122 and Glu309 are depicted with a ball-and-stick model (blue for the active form and red for the inactive form). (c) The pH-sensitive Glu122 adopts two conformations.

Figure 6.
Figure 6. A proposed reaction mechanism for ChoK.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 785-795) copyright 2004.

Figures were selected by an automated process.