6OXC

Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1126/science.aay0934
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylmalonyl-CoA mutase large subunit750Mycobacterium tuberculosisMutation(s): 0 
Gene Names: mutBDK316_08225DSI35_00620ERS027651_01113ERS027652_00280ERS124361_00189SAMEA2682864_01878SAMEA2683035_01024
EC: 5.4.99.2
UniProt
Find proteins for P9WJK5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJK5 
Go to UniProtKB:  P9WJK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJK5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methylmalonyl-CoA mutase small subunit mutA616Mycobacterium tuberculosisMutation(s): 1 
Gene Names: mutAERS007663_02000ERS023446_02236ERS027651_01114ERS027656_01366ERS124361_00188SAMEA2682864_01877SAMEA2683035_01025
EC: 5.4.99.2
UniProt
Find proteins for P9WJK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJK7 
Go to UniProtKB:  P9WJK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJK7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.802α = 90
b = 103.561β = 90
c = 211.197γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • 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