Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.55 kDa 
• Atom Count: 5129 
• Residue Count: 570 
• Unique protein chains: 1

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 

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 
• 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

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
Find proteins for Q9AMP1 (Vibrio harveyi) Explore Q9AMP1  Go to UniProtKB:  Q9AMP1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PNX	A	3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE C13 H18 N4 O3 BYPFEZZEUUWMEJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PNX	Kd :  600000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.195 
• R-Value Work: 0.143 
• R-Value Observed: 0.146 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.67	α = 90
b = 83.93	β = 90
c = 102.42	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

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

Revision History 

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-01-29
  Changes: Database references