6OXC | pdb_00006oxc

Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin

• PDB DOI: https://doi.org/10.2210/pdb6OXC/pdb

• Classification: ISOMERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-05-13 Released: 2019-11-13 
• Deposition Author(s): Purchal, M., Ruetz, M., Banerjee, R., Koutmos, M.
• Funding Organization(s): American Heart Association, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair.

Ruetz, M., Campanello, G.C., Purchal, M., Shen, H., McDevitt, L., Gouda, H., Wakabayashi, S., Zhu, J., Rubin, E.J., Warncke, K., Mootha, V.K., Koutmos, M., Banerjee, R.

(2019) Science 366: 589-593

• PubMed: 31672889 
• DOI: https://doi.org/10.1126/science.aay0934
• Primary Citation Related Structures: 
  6OXC, 6OXD


• PubMed Abstract: 
  

  Itaconate is an immunometabolite with both anti-inflammatory and bactericidal effects. Its coenzyme A (CoA) derivative, itaconyl-CoA, inhibits B ₁₂ -dependent methylmalonyl-CoA mutase (MCM) by an unknown mechanism. We demonstrate that itaconyl-CoA is a suicide inactivator of human and Mycobacterium tuberculosis MCM, which forms a markedly air-stable biradical adduct with the 5'-deoxyadenosyl moiety of the B ₁₂ coenzyme. Termination of the catalytic cycle in this way impairs communication between MCM and its auxiliary repair proteins. Crystallography and spectroscopy of the inhibited enzyme are consistent with a metal-centered cobalt radical ~6 angstroms away from the tertiary carbon-centered radical and suggest a means of controlling radical trajectories during MCM catalysis. Mycobacterial MCM thus joins enzymes in the glyoxylate shunt and the methylcitrate cycle as targets of itaconate in pathogen propionate metabolism.

---

Organizational Affiliation: 
• Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
Broad Institute, Cambridge, MA 02142, USA.
Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Cambridge, MA 02115, USA.
Department of Physics, Emory University, Atlanta, GA 30322, USA.
Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 147.14 kDa 
• Atom Count: 11,431 
• Modeled Residue Count: 1,323 
• Deposited Residue Count: 1,366 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylmalonyl-CoA mutase large subunit	A	750	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: mutB, DK316_08225, DSI35_00620, ERS027651_01113, ERS027652_00280, ERS124361_00189, SAMEA2682864_01878, SAMEA2683035_01024 EC: 5.4.99.2
UniProt
Find proteins for P9WJK5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJK5  Go to UniProtKB:  P9WJK5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylmalonyl-CoA mutase small subunit mutA	B	616	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: mutA, ERS007663_02000, ERS023446_02236, ERS027651_01114, ERS027656_01366, ERS124361_00188, SAMEA2682864_01877, SAMEA2683035_01025 EC: 5.4.99.2
UniProt
Find proteins for P9WJK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJK7  Go to UniProtKB:  P9WJK7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12	C [auth A]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
5AD	D [auth A]	5'-DEOXYADENOSINE C10 H13 N5 O3 XGYIMTFOTBMPFP-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.802	α = 90
b = 103.561	β = 90
c = 211.197	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Purchal, M., Ruetz, M., Banerjee, R., Koutmos, M.

---

Funding Organization	Location	Grant Number
American Heart Association	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description