4ZQR

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
A, B, C, D
407Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: guaBguaB2Rv3411cMTCY78.17
EC: 1.1.1.205
UniProt
Find proteins for P9WKI7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKI7 
Go to UniProtKB:  P9WKI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKI7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
HA [auth D],
P [auth B],
Z [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
GA [auth D]
J [auth A]
BA [auth C],
CA [auth C],
DA [auth C],
GA [auth D],
J [auth A],
K [auth A],
L [auth A],
LA [auth D],
N [auth A],
S [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
PGO
Query on PGO

Download Ideal Coordinates CCD File 
AA [auth C]
EA [auth C]
F [auth A]
FA [auth D]
G [auth A]
AA [auth C],
EA [auth C],
F [auth A],
FA [auth D],
G [auth A],
H [auth A],
I [auth A],
IA [auth D],
JA [auth D],
KA [auth D],
Q [auth B],
R [auth B],
U [auth B],
V [auth B],
Y [auth C]
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
K
Query on K

Download Ideal Coordinates CCD File 
M [auth A],
O [auth A],
T [auth B],
X [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/m34zqr
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.217α = 108.3
b = 75.233β = 108.25
c = 75.291γ = 111.88
Software Package:
Software NamePurpose
PHENIXrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000phasing
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United 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
  • Version 1.4: 2022-03-30
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.5: 2024-05-22
    Changes: Data collection