6JCM

Crystal structure of ligand-free Rv0187.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural and biochemical characterization of Rv0187, an O-methyltransferase from Mycobacterium tuberculosis.

Lee, S.Kang, J.Kim, J.

(2019) Sci Rep 9: 8059-8059

  • DOI: https://doi.org/10.1038/s41598-019-44592-7
  • Primary Citation of Related Structures:  
    6JCL, 6JCM

  • PubMed Abstract: 

    Catechol O-methyltransferase (COMT) is widely distributed in nature and installs a methyl group onto one of the vicinal hydroxyl groups of a catechol derivative. Enzymes belonging to this family require two cofactors for methyl transfer: S-adenosyl-l-methionine as a methyl donor and a divalent metal cation for regiospecific binding and activation of a substrate. We have determined two high-resolution crystal structures of Rv0187, one of three COMT paralogs from Mycobacterium tuberculosis, in the presence and absence of cofactors. The cofactor-bound structure clearly locates strontium ions and S-adenosyl-l-homocysteine in the active site, and together with the complementary structure of the ligand-free form, it suggests conformational dynamics induced by the binding of cofactors. Examination of in vitro activities revealed promiscuous substrate specificity and relaxed regioselectivity against various catechol-like compounds. Unexpectedly, mutation of the proposed catalytic lysine residue did not abolish activity but altered the overall landscape of regiospecific methylation.


  • Organizational Affiliation

    Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable O-methyltransferase
A, B, C, D
248Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv0187
EC: 2.1.1.6
UniProt
Find proteins for O07431 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O07431 
Go to UniProtKB:  O07431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO07431
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.333α = 90
b = 94.262β = 90
c = 125.677γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2016R1D1A1B03930716

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description