1ZFJ

INOSINE MONOPHOSPHATE DEHYDROGENASE (IMPDH; EC 1.1.1.205) FROM STREPTOCOCCUS PYOGENES

PDB DOI: 10.2210/pdb1ZFJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptococcus pyogenes
Expression System: Streptococcus pyogenes
Mutation(s): Yes

Deposited: 1999-03-29 Released: 2000-03-29
Deposition Author(s): Zhang, R., Evans, G., Rotella, F.J., Westbrook, E.M., Beno, D., Huberman, E., Joachimiak, A., Collart, F.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.263
R-Value Work: 0.232

wwPDB Validation 3D Report Full Report

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

Literature

Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase.

Zhang, R., Evans, G., Rotella, F.J., Westbrook, E.M., Beno, D., Huberman, E., Joachimiak, A., Collart, F.R.

(1999) Biochemistry 38: 4691-4700

PubMed: 10200156 Search on PubMed
DOI: 10.1021/bi982858v
Primary Citation of Related Structures:
1ZFJ

PubMed Abstract:

IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the first step unique to GTP synthesis. To provide a basis for the evaluation of IMPDH inhibitors as antimicrobial agents, we have expressed and characterized IMPDH from the pathogenic bacterium Streptococcus pyogenes. Our results show that the biochemical and kinetic characteristics of S. pyogenes IMPDH are similar to other bacterial IMPDH enzymes. However, the lack of sensitivity to mycophenolic acid and the Km for NAD (1180 microM) exemplify some of the differences between the bacterial and mammalian IMPDH enzymes, making it an attractive target for antimicrobial agents. To evaluate the basis for these differences, we determined the crystal structure of the bacterial enzyme at 1.9 A with substrate bound in the catalytic site. The structure was determined using selenomethionine-substituted protein and multiwavelength anomalous (MAD) analysis of data obtained with synchrotron radiation from the undulator beamline (19ID) of the Structural Biology Center at Argonne's Advanced Photon Source. S. pyogenes IMPDH is a tetramer with its four subunits related by a crystallographic 4-fold axis. The protein is composed of two domains: a TIM barrel domain that embodies the catalytic framework and a cystathione beta-synthase (CBS) dimer domain of so far unknown function. Using information provided by sequence alignments and the crystal structure, we prepared several site-specific mutants to examine the role of various active site regions in catalysis. These variants implicate the active site flap as an essential catalytic element and indicate there are significant differences in the catalytic environment of bacterial and mammalian IMPDH enzymes. Comparison of the structure of bacterial IMPDH with the known partial structures from eukaryotic organisms will provide an explanation of their distinct properties and contribute to the design of specific bacterial IMPDH inhibitors.

Organizational Affiliation:

Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439-4833, USA. Fcollart@anl.gov

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INOSINE MONOPHOSPHATE DEHYDROGENASE	A	491	Streptococcus pyogenes	Mutation(s): 13 Gene Names: guaB, impD EC: 1.1.1.205
UniProt
Find proteins for P0C0H6 (Streptococcus pyogenes) Explore P0C0H6 Go to UniProtKB: P0C0H6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0H6
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.263
R-Value Work: 0.232
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.48	α = 90
b = 151.48	β = 90
c = 101.68	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CCP4	model building
HKL-2000	data reduction
DENZO	data reduction
HKL-2000	data scaling
SCALEPACK	data scaling
CNS	phasing
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 1999-03-29
Released Date: 2000-03-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-03-29
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance