Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA small subunit methyltransferase C
Synonym: YjjT
GI: 732118
Orf: yjjT, b4371
COG: COG2813
UniProt: P39406
Structures: | 2PJD |
Enzyme type: methyltransferase
Position of modification - modification: s:1207(1207) - m2G


PDB Structures:


2PJD

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

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.

Download RCSB-PDB Structures:

Pdb Files   2PJD.pdb  
Pdbx/mmCIF Files   2PJD.cif  


Protein sequence:

MSAFTPASEVLLRHSDDFEQSRILFAGDLQDDLPARLDTAASRAHTQQFHHWQVLSRQMGDNARFSLVATADDVADCDTLIYYWPKNKPEAQFQLMNLLSLLPVGTDIFVVGENRSGVRSAEQMLADYAPLNKVDSARRCGLYFGRLEKQPVFDAEKFWGEYSVDGLTVKTLPGVFSRDGLDVGSQLLLSTLTPHTKGKVLDVGCGAGVLSVAFARHSPKIRLTLCDVSAPAVEASRATLAANGVEGEVFASNVFSEVKGRFDMIISNPPFHDGMQTSLDAAQTLIRGAVRHLNSGGELRIVANAFLPYPDVLDETFGFHEVIAQTGRFKVYRAIMTRQAKKG

Comments:

RsmC catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to G1207 in hairpin 34 of 16S rRNA (m2G1207). It has two homologous domains tandemly duplicated within a single polypeptide. The enzyme reacts well with 30S subunits reconstituted from 16S RNA transcripts and 30S proteins, but is almost inactive with the corresponding free RNA. E. coli RsmC is closely related to E. coli RsmD (m2G966/16S rRNA) and also to a family of other MTases from Gram-positive bacteria and Archaea, typified by the Mj0882 protein from M. jannaschii (1dus in PDB) (The acronym RsmC has also been used for for ‘Regulator of Secondary Metabolism C’, a protein not related to Ribosomal small subunit Methyltransferase C).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m2G RNA rRNA 1207 SSU-16S Prokaryotic Cytosol



Publications:

Title Authors Journal Details PubMed Id DOI
Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J Nucleic Acids Res [details] 17576679 -
Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases. Bujnicki JM FASEB J [details] 11053259 -
Ribosomal RNA guanine-(N2)-methyltransferases and their targets. Sergiev PV, Bogdanov AA, Dontsova OA Nucleic Acids Res [details] 17389639 -
RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. Bujnicki JM, Rychlewski L BMC Bioinformatics [details] 11929612 -
Purification, cloning, and characterization of the 16 S RNA m2G1207 methyltransferase from Escherichia coli. Tscherne JS, Nurse K, Popienick P, Ofengand J J Biol Chem [details] 9873033 -

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