4ZQR | pdb_00004zqr

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

• PDB DOI: https://doi.org/10.2210/pdb4ZQR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-11 Released: 2015-06-17 
• Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Kavitha, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

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

• PubMed: 26440283 
• DOI: https://doi.org/10.1371/journal.pone.0138976
• Primary Citation 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.
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.
Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America.
Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America.
Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN, United States of America.
Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 549A Science and Research Building 2, Houston, TX, United States of America; Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, United States of America.
Department of Biology, Brandeis University, 415 South St. Waltham, MA, United States of America; Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, United States of America.

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: 169.26 kDa 
• Atom Count: 11,793 
• Modeled Residue Count: 1,429 
• Deposited Residue Count: 1,628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase	A, B, C, D	407	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: guaB, guaB2, Rv3411c, MTCY78.17 EC: 1.1.1.205
UniProt
Find proteins for P9WKI7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKI7  Go to UniProtKB:  P9WKI7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], HA [auth D], P [auth B], Z [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	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	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	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 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34zqr

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.217	α = 108.3
b = 75.233	β = 108.25
c = 75.291	γ = 111.88

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Kavitha, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• 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