3ARU

Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - W275G mutant complex structure with PENTOXIFYLLINE

DOI: 10.2210/pdb3ARU/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Vibrio harveyi
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-12-09 Released: 2011-04-20
Deposition Author(s): Pantoom, S., Vetter, I.R., Prinz, H., Suginta, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.195
R-Value Work: 0.143
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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

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

(2011) J Biol Chem 286: 24312-24323

PubMed: 21531720 Search on PubMedSearch on PubMed Central
DOI: 10.1074/jbc.M110.183376
Primary Citation of Related Structures:
3ART, 3ARU, 3ARV, 3ARW, 3ARX, 3ARY, 3ARZ, 3ARO, 3AS0, 3ARP

PubMed 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.

Related Citations:

Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism
Songsiriritthigul, C., Pantoom, S., Aguda, A.H., Robinson, R.C., Suginta, W.
(2008) J Struct Biol 162: 491

Organizational Affiliation:

Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase A	A	584	Vibrio harveyi	Mutation(s): 1 Gene Names: chiA EC: 3.2.1.14
UniProt
Find proteins for Q9AMP1 (Vibrio harveyi) Explore Q9AMP1 Go to UniProtKB: Q9AMP1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PNX Query on PNX Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE C₁₃ H₁₈ N₄ O₃ BYPFEZZEUUWMEJ-UHFFFAOYSA-N		Ligand Interaction