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Escherichia coli K-12 substr. MG1655 Enzyme: 16S rRNA m2G1207 methyltransferase



Gene: rsmC Accession Numbers: G7950 (EcoCyc), b4371, ECK4362

Synonyms: yjjT, ribosomal RNA small subunit methyltransferase C

Regulation Summary Diagram: ?

Summary:
RsmC is the methyltransferase responsible for methylation of 16S rRNA at the N2 position of the G1207 nucleotide. In vitro, the enzyme can methylate 16S rRNA within the 30S ribosomal subunit, but not free 16S rRNA [Tscherne99a].

The C-terminal domain of RsmC is conserved across many known and predicted N-methyltransferases. The N-terminal domain also has some similarity with this conserved domain, but is missing all the residues predicted to be required for methyltransferase activity [Bujnicki02]. A crystal structure of RsmC has been solved at 2.1 Å resolution, confirming structural similarity of the N- and C-terminal domains, and thus domain duplication. The C-terminal domain may require presence of the N-terminal domain for proper folding [Sunita07].

Point mutants in various predicted active site residues show reduced activity [Sunita07].

Review: [Sergiev07]

Locations: cytosol

Map Position: [4,604,692 <- 4,605,723] (99.25 centisomes)
Length: 1032 bp / 343 aa

Molecular Weight of Polypeptide: 37.625 kD (from nucleotide sequence), 37.0 kD (experimental) [Tscherne99a ]

Unification Links: ASAP:ABE-0014336 , DIP:DIP-10804N , EchoBASE:EB2481 , EcoGene:EG12596 , EcoliWiki:b4371 , ModBase:P39406 , OU-Microarray:b4371 , PortEco:rsmC , PR:PRO_000023883 , Pride:P39406 , Protein Model Portal:P39406 , RefSeq:NP_418788 , RegulonDB:G7950 , SMR:P39406 , String:511145.b4371 , UniProt:P39406

Relationship Links: InterPro:IN-FAMILY:IPR002052 , InterPro:IN-FAMILY:IPR007848 , InterPro:IN-FAMILY:IPR013675 , InterPro:IN-FAMILY:IPR023543 , PDB:Structure:2PJD , Pfam:IN-FAMILY:PF05175 , Pfam:IN-FAMILY:PF08468

In Paralogous Gene Group: 194 (13 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0031167 - rRNA methylation Inferred from experiment [Tscherne99a]
GO:0070475 - rRNA base methylation Inferred from experiment [Sunita07]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0008990 - rRNA (guanine-N2-)-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01, Tscherne99a]
GO:0052914 - 16S rRNA (guanine(1207)-N(2))-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01a, Tscherne99a]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0008649 - rRNA methyltransferase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by curator Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Tscherne99a]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rsmC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Curated 15-Feb-2006 by Shearer A , SRI International
Last-Curated ? 23-Sep-2008 by Keseler I , SRI International


Enzymatic reaction of: 16S rRNA m2G1207 methyltransferase

EC Number: 2.1.1.172

S-adenosyl-L-methionine + guanine1207 in 16S rRNA <=> S-adenosyl-L-homocysteine + N2-methylguanine1207 in 16S rRNA + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Mg2+ [Tscherne99a]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Tscherne99a]
 
Chain 2 -> 343
[UniProt09]
UniProt: Ribosomal RNA small subunit methyltransferase C;
Mutagenesis-Variant 86
[Sunita07, UniProt11a]
Alternate sequence: K → S; UniProt: Reduces activity by 84%; when associated with S-88.
Mutagenesis-Variant 88
[Sunita07, UniProt11a]
Alternate sequence: K → S; UniProt: Reduces activity by 84%; when associated with S-86.
Mutagenesis-Variant 202
[Sunita07, UniProt11a]
Alternate sequence: D → A; UniProt: Abolishes affinity for S-adenosyl- L-methionine. Loss of activity.
Mutagenesis-Variant 227
[Sunita07, UniProt11a]
Alternate sequence: D → A; UniProt: Strongly reduces affinity for S- adenosyl-L-methionine. Reduces activity by 87%.
Mutagenesis-Variant 268
[Sunita07, UniProt11a]
Alternate sequence: N → A; UniProt: Reduces affinity for S-adenosyl-L- methionine. Reduces activity by 80%.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bujnicki02: Bujnicki JM, Rychlewski L (2002). "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." BMC Bioinformatics 3;10. PMID: 11929612

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Sergiev07: Sergiev PV, Bogdanov AA, Dontsova OA (2007). "Ribosomal RNA guanine-(N2)-methyltransferases and their targets." Nucleic Acids Res 35(7):2295-301. PMID: 17389639

Sunita07: Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J (2007). "Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC." Nucleic Acids Res 35(13);4264-74. PMID: 17576679

Tscherne99a: Tscherne JS, Nurse K, Popienick P, Ofengand J (1999). "Purification, cloning, and characterization of the 16 S RNA m2G1207 methyltransferase from Escherichia coli." J Biol Chem 274(2);924-9. PMID: 9873033

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Thu Nov 27, 2014, BIOCYC13B.