2PJD

Crystal structure of 16S rRNA methyltransferase RsmC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC

Sunita, S.Purta, E.Durawa, M.Tkaczuk, K.L.Swaathi, J.Bujnicki, J.M.Sivaraman, J.

(2007) Nucleic Acids Res. 35: 4264-4274

  • DOI: 10.1093/nar/gkm411

  • PubMed Abstract: 
  • RNA methyltransferases (MTases) are important players in the biogenesis and regulation of the ribosome, the cellular machine for protein synthesis. RsmC is a MTase that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to G1 ...

    RNA methyltransferases (MTases) are important players in the biogenesis and regulation of the ribosome, the cellular machine for protein synthesis. RsmC is a MTase that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to G1207 of 16S rRNA. Mutations of G1207 have dominant lethal phenotypes in Escherichia coli, underscoring the significance of this modified nucleotide for ribosome function. Here we report the crystal structure of E. coli RsmC refined to 2.1 A resolution, which reveals two homologous domains tandemly duplicated within a single polypeptide. We characterized the function of the individual domains and identified key residues involved in binding of rRNA and SAM, and in catalysis. We also discovered that one of the domains is important for the folding of the other. Domain duplication and subfunctionalization by complementary degeneration of redundant functions (in particular substrate binding versus catalysis) has been reported for many enzymes, including those involved in RNA metabolism. Thus, RsmC can be regarded as a model system for functional streamlining of domains accompanied by the development of dependencies concerning folding and stability.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA small subunit methyltransferase C
A
343Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rsmC (yjjT)
EC: 2.1.1.172
Find proteins for P39406 (Escherichia coli (strain K12))
Go to UniProtKB:  P39406
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.939α = 90.00
b = 51.503β = 121.52
c = 73.330γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2007-10-12
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance