Rv2966c of M. tuberculosis is a RsmD-like methyltransferase

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Structural and functional characterization of Rv2966c protein reveals an RsmD-like methyltransferase from Mycobacterium tuberculosis and the role of its N-terminal domain in target recognition

Kumar, A.Saigal, K.Malhotra, K.Sinha, K.M.Taneja, B.

(2011) J Biol Chem 286: 19652-19661

  • DOI: https://doi.org/10.1074/jbc.M110.200428
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Nine of ten methylated nucleotides of Escherichia coli 16 S rRNA are conserved in Mycobacterium tuberculosis. All the 10 different methyltransferases are known in E. coli, whereas only TlyA and GidB have been identified in mycobacteria. Here we have identified Rv2966c of M. tuberculosis as an ortholog of RsmD protein of E. coli. We have shown that rv2966c can complement rsmD-deleted E. coli cells. Recombinant Rv2966c can use 30 S ribosomes purified from rsmD-deleted E. coli as substrate and methylate G966 of 16 S rRNA in vitro. Structure determination of the protein shows the protein to be a two-domain structure with a short hairpin domain at the N terminus and a C-terminal domain with the S-adenosylmethionine-MT-fold. We show that the N-terminal hairpin is a minimalist functional domain that helps Rv2966c in target recognition. Deletion of the N-terminal domain prevents binding to nucleic acid substrates, and the truncated protein fails to carry out the m(2)G966 methylation on 16 S rRNA. The N-terminal domain also binds DNA efficiently, a property that may be utilized under specific conditions of cellular growth.

  • Organizational Affiliation

    Institute of Genomics and Integrative Biology (Council of Scientific and Industrial Research), Delhi, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POSSIBLE METHYLTRANSFERASE (METHYLASE)189Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: MT3044Rv2966c
EC: 2.1.1
Find proteins for I6XFS7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6XFS7 
Go to UniProtKB:  I6XFS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6XFS7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.78α = 90
b = 54.78β = 90
c = 100.04γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-02
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description