6MJY

M. thermoresistible GuaB2 delta-CBS in complex with 6Cl-IMP

• PDB DOI: https://doi.org/10.2210/pdb6MJY/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor
• Organism(s): Mycolicibacterium thermoresistibile
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-09-23 Released: 2019-09-25 
• Deposition Author(s): Ascher, D.B., Pacitto, A., Blundell, T.L.
• Funding Organization(s): European Union (EU), Medical Research Council (MRC, United Kingdom), National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.191 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH).

Trapero, A., Pacitto, A., Chan, D.S., Abell, C., Blundell, T.L., Ascher, D.B., Coyne, A.G.

(2020) Bioorg Med Chem Lett 30: 126792-126792

• PubMed: 31757668 
• DOI: https://doi.org/10.1016/j.bmcl.2019.126792
• Primary Citation of Related Structures:  
  6MJY


• PubMed Abstract: 
  

  Inosine-5'-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme involved in nucleotide biosynthesis. Because of its critical role in purine biosynthesis, IMPDH is a drug design target for immunosuppressive, anticancer, antiviral and antimicrobial chemotherapy. In this study, we use mass spectrometry and X-ray crystallography to show that the inhibitor 6-Cl-purine ribotide forms a covalent adduct with the Cys-341 residue of Mycobacterium thermoresistibile IMPDH.

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Organizational Affiliation: 

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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)

Biological Assembly Evidence: gel filtration, light scattering, equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 40.22 kDa 
• Atom Count: 2,469 
• Modelled Residue Count: 315 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A	389	Mycolicibacterium thermoresistibile	Mutation(s): 0  Gene Names: guaB, RMCT_0580 EC: 1.1.1.205
UniProt
Find proteins for G7CNL4 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CNL4  Go to UniProtKB:  G7CNL4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPR (Subject of Investigation/LOI)	B [auth A]	6-CHLOROPURINE RIBOSIDE, 5'-MONOPHOSPHATE C10 H13 Cl N4 O7 P ALOBOMYIOYNCBS-KQYNXXCUSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.191 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.53	α = 90
b = 88.53	β = 90
c = 84.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Ascher, D.B., Pacitto, A., Blundell, T.L.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	260872
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/M026302/1
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1072476

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2020-04-08
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description