PDBsum entry 3as2

Hydrolase/hydrolase inhibitor

PDB id: 3as2

Contents

Protein chain

570 a.a.

Ligands

POY ×3

Waters ×588

PDB id:

3as2

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure analysis of chitinase a from vibrio harveyi with novel inhibitors - w275g mutant complex structure with propentofylline

Structure:

Chitinase a. Chain: a. Fragment: residues 22-597. Engineered: yes. Mutation: yes

Source:

Vibrio harveyi. Organism_taxid: 669. Strain: lmg7890. Gene: chia. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.149 R-free: 0.193

Authors:

S.Pantoom,I.R.Vetter,H.Prinz,W.Suginta

Key ref:

S.Pantoom et al. (2011). Potent family-18 chitinase inhibitors: x-ray structures, affinities, and binding mechanisms. J Biol Chem, 286, 24312-24323. PubMed id: 21531720

Date:

09-Dec-10 Release date: 20-Apr-11

Protein chain

Q9AMP1  (Q9AMP1_VIBHA) -  chitinase from Vibrio harveyi

Seq: 850 a.a.

Struc: 570 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.2.1.14 - chitinase.
• Reaction: Hydrolysis of the 1,4-beta-linkages of N-acetyl-D-glucosamine polymers of chitin.

J Biol Chem 286:24312-24323 (2011)

PubMed id: 21531720

Potent family-18 chitinase inhibitors: x-ray structures, affinities, and binding mechanisms.

S.Pantoom, I.R.Vetter, H.Prinz, W.Suginta.

ABSTRACT

Six novel inhibitors of Vibrio harveyi chitinase A (VhChiA), a family-18 chitinase homolog, were identified by in vitro screening of a library of pharmacologically active compounds. Unlike the previously identified inhibitors that mimicked the reaction intermediates, crystallographic evidence from 14 VhChiA-inhibitor complexes showed that all of the inhibitor molecules occupied the outer part of the substrate-binding cleft at two hydrophobic areas. The interactions at the aglycone location are well defined and tightly associated with Trp-397 and Trp-275, whereas the interactions at the glycone location are patchy, indicating lower affinity and a loose interaction with two consensus residues, Trp-168 and Val-205. When Trp-275 was substituted with glycine (W275G), the binding affinity toward all of the inhibitors dramatically decreased, and in most structures two inhibitor molecules were found to stack against Trp-397 at the aglycone site. Such results indicate that hydrophobic interactions are important for binding of the newly identified inhibitors by the chitinase. X-ray data and isothermal microcalorimetry showed that the inhibitors occupied the active site of VhChiA in three different binding modes, including single-site binding, independent two-site binding, and sequential two-site binding. The inhibitory effect of dequalinium in the low nanomolar range makes this compound an extremely attractive lead compound for plausible development of therapeutics against human diseases involving chitinase-mediated pathologies.