6JCL

Crystal structure of cofactor-bound Rv0187 from MTB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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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. jwkim@gist.ac.kr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable O-methyltransferase235Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv0187
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
EA [auth H]
GA [auth E]
I [auth A]
IA [auth F]
N [auth B]
EA [auth H],
GA [auth E],
I [auth A],
IA [auth F],
N [auth B],
T [auth C],
V [auth D],
Z [auth G]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth G]
FA [auth H]
HA [auth E]
JA [auth F]
K [auth A]
BA [auth G],
FA [auth H],
HA [auth E],
JA [auth F],
K [auth A],
P [auth B],
Q [auth B],
U [auth C],
X [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SR (Subject of Investigation/LOI)
Query on SR

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth G]
DA [auth G]
J [auth A]
L [auth A]
AA [auth G],
CA [auth G],
DA [auth G],
J [auth A],
L [auth A],
M [auth A],
O [auth B],
S [auth B],
W [auth D],
Y [auth D]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
R [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH Binding MOAD:  6JCL Kd: 1.25e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.3α = 90
b = 75.92β = 90
c = 329.839γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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, Derived calculations, Refinement description