4ZQM

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with XMP and NAD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds.

Makowska-Grzyska, M., Kim, Y., Gorla, S.K., Wei, Y., Mandapati, K., Zhang, M., Maltseva, N., Modi, G., Boshoff, H.I., Gu, M., Aldrich, C., Cuny, G.D., Hedstrom, L., Joachimiak, A.

(2015) PLoS One 10: e0138976-e0138976

  • DOI: 10.1371/journal.pone.0138976
  • Primary Citation of Related Structures:  
    4ZQM, 4ZQN, 4ZQO, 4ZQP, 4ZQR

  • PubMed Abstract: 

    • Tuberculosis (TB) remains a worldwide problem and the need for new drugs is increasingly more urgent with the emergence of multidrug- and extensively-drug resistant TB. Inosine 5'-monophosphate dehydrogenase 2 (IMPDH2) from Mycobacterium tuberculosis (Mtb) is an attractive drug target ...

    Tuberculosis (TB) remains a worldwide problem and the need for new drugs is increasingly more urgent with the emergence of multidrug- and extensively-drug resistant TB. Inosine 5'-monophosphate dehydrogenase 2 (IMPDH2) from Mycobacterium tuberculosis (Mtb) is an attractive drug target. The enzyme catalyzes the conversion of inosine 5'-monophosphate into xanthosine 5'-monophosphate with the concomitant reduction of NAD+ to NADH. This reaction controls flux into the guanine nucleotide pool. We report seventeen selective IMPDH inhibitors with antitubercular activity. The crystal structures of a deletion mutant of MtbIMPDH2 in the apo form and in complex with the product XMP and substrate NAD+ are determined. We also report the structures of complexes with IMP and three structurally distinct inhibitors, including two with antitubercular activity. These structures will greatly facilitate the development of MtbIMPDH2-targeted antibiotics.

    Organizational Affiliation: 

    Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America; Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL, United States of America.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase A407Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: guaB, guaB2, Rv3411c, MTCY78.17
EC: 1.1.1.205
Find proteins for P9WKI7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKI7 
Go to UniProtKB:  P9WKI7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
XMP
Query on XMP
Download Ideal Coordinates CCD File 
A
XANTHOSINE-5'-MONOPHOSPHATE
C10 H14 N4 O9 P
DCTLYFZHFGENCW-UUOKFMHZSA-O		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: I 4
  • Diffraction Data DOI: 10.18430/M34ZQM Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.154α = 90
b = 88.154β = 90
c = 85.512γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
SBC-Collectdata collection
HKL-3000phasing
HKL-3000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Structure summary
  • Version 1.3: 2017-11-22
    Changes: Refinement description