Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.90 kDa 
• Atom Count: 2719 
• Residue Count: 334 
• Unique protein chains: 1

2PJD

Crystal structure of 16S rRNA methyltransferase RsmC

• DOI: 10.2210/pdb2PJD/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-16 Released: 2007-07-03 
• Deposition Author(s): Sunita, S., Purta, E., Durawa, M., Tkaczuk, K.L., Bujnicki, J.M., Sivaraman, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.204 
• R-Value Observed: 0.256 

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

• PubMed: 17576679 
• DOI: 10.1093/nar/gkm411
• Primary Citation of Related Structures:  
  2PJD


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA small subunit methyltransferase C	A	343	Escherichia coli	Mutation(s): 0  Gene Names: rsmC EC: 2.1.1.52 (PDB Primary Data), 2.1.1.172 (UniProt)
Find proteins for P39406 (Escherichia coli (strain K12)) Explore P39406  Go to UniProtKB:  P39406

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.204 
• R-Value Observed: 0.256 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.939	α = 90
b = 51.503	β = 121.52
c = 73.33	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
SHARP	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-16 
• Released Date: 2007-07-03 
Deposition Author(s): Sunita, S., Purta, E., Durawa, M., Tkaczuk, K.L., Bujnicki, J.M., Sivaraman, J.

Revision History 

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