3ZFH | pdb_00003zfh

Crystal structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb3ZFH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-11 Released: 2013-01-16 
• Deposition Author(s): Rao, V.A., Shepherd, S.M., Owen, R., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.190 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.148 (Depositor) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Structure of Pseudomonas Aeruginosa Inosine 5'-Monophosphate Dehydrogenase

Rao, V.A., Shepherd, S.M., Owen, R., Hunter, W.N.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 243

• PubMed: 23519796 
• DOI: https://doi.org/10.1107/S1744309113002352
• Primary Citation Related Structures: 
  3ZFH


• PubMed Abstract: 
  

  Inosine 5'-monophosphate dehydrogenase (IMPDH) represents a potential antimicrobial drug target. The crystal structure of recombinant Pseudomonas aeruginosa IMPDH has been determined to a resolution of 2.25 Å. The structure is a homotetramer of subunits dominated by a (β/α)8-barrel fold, consistent with other known structures of IMPDH. Also in common with previous work, the cystathionine β-synthase domains, residues 92-204, are not present in the model owing to disorder. However, unlike the majority of available structures, clearly defined electron density exists for a loop that creates part of the active site. This loop, composed of residues 297-315, links α8 and β9 and carries the catalytic Cys304. P. aeruginosa IMPDH shares a high level of sequence identity with bacterial and protozoan homologues, with residues involved in binding substrate and the NAD+ cofactor being conserved. Specific differences that have been proven to contribute to selectivity against the human enzyme in a study of Cryptosporidium parvum IMPDH are also conserved, highlighting the potential value of IMPDH as a drug target.

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Organizational Affiliation: 
• Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 54.22 kDa 
• Atom Count: 2,298 
• Modeled Residue Count: 299 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INOSINE 5'-MONOPHOSPHATE DEHYDROGENASE	A	510	Pseudomonas aeruginosa PAO1	Mutation(s): 0  EC: 1.1.1.205
UniProt
Find proteins for Q9HXM5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXM5  Go to UniProtKB:  Q9HXM5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.190 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.148 (Depositor) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.546	α = 90
b = 115.546	β = 90
c = 56.443	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Rao, V.A., Shepherd, S.M., Owen, R., Hunter, W.N.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2013-03-13
  Changes: Database references
• Version 1.2: 2013-04-17
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description