4L69

Rv2372c of Mycobacterium tuberculosis is RsmE like methyltransferse


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The structure of Rv2372c identifies an RsmE-like methyltransferase from Mycobacterium tuberculosis

Kumar, A.Kumar, S.Taneja, B.

(2014) Acta Crystallogr.,Sect.D 70: 821-832

  • DOI: 10.1107/S1399004713033555

  • PubMed Abstract: 
  • U1498 of 16S rRNA plays an important role in translation fidelity as well as in antibiotic response. U1498 is present in a methylated form in the decoding centre of the ribosome. In this study, Rv2372c from Mycobacterium tuberculosis has been identif ...

    U1498 of 16S rRNA plays an important role in translation fidelity as well as in antibiotic response. U1498 is present in a methylated form in the decoding centre of the ribosome. In this study, Rv2372c from Mycobacterium tuberculosis has been identified as an RsmE-like methyltransferase which specifically methylates U1498 of 16S rRNA at the N3 position and can complement RsmE-deleted Escherichia coli. The crystal structure of Rv2372c has been determined, and reveals that the protein belongs to a distinct class in the SPOUT superfamily and exists as a dimer. The deletion of critical residues at the C-terminus of Rv2372c leads to an inability of the protein to form stable dimers and to abolition of the methyltransferase activity. A ternary model of Rv2372c with its cofactor S-adenosylmethionine (SAM) and the 16S rRNA fragment (1487)16S rRNA(1510) helps to identify binding pockets for SAM (in the deep trefoil knot) and substrate RNA (at the dimer interface) and suggests an S(N)2 mechanism for the methylation of N3 of U1498 in 16S rRNA.


    Organizational Affiliation

    Structural Biology Unit, CSIR - Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110 020, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA small subunit methyltransferase E
A
263Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: rsmE
EC: 2.1.1.193
Find proteins for P9WGX1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGX1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.940α = 90.00
b = 81.940β = 90.00
c = 115.070γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOSFLMdata reduction
BUSTERrefinement
BALBESphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-12 
  • Released Date: 2014-03-19 
  • Deposition Author(s): Kumar, A., Taneja, B.

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release