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Escherichia coli K-12 substr. MG1655 Enzyme: 16S rRNA m3U1498 methyltransferase

Gene: rsmE Accession Numbers: EG12366 (EcoCyc), b2946, ECK2941

Synonyms: yggJ, ribosomal RNA small subunit methyltransferase E

Regulation Summary Diagram

Regulation summary diagram for rsmE

Subunit composition of 16S rRNA m3U1498 methyltransferase = [RsmE]2
         16S rRNA m3U1498 methyltransferase monomer = RsmE

RsmE is the methyltransferase responsible for methylation of 16S rRNA at the N3 position of the U1498 nucleotide [Basturea06]. In vitro, RsmE can methylate 16S rRNA within the assembled 30S ribosomal subunit, but not 70S ribosomes or naked 16S rRNA [Basturea07]. RsmE belongs to the DUF family of predicted α/β trefoil knot methyltransferases [Basturea06].

A strain carrying a deletion of rsmE appears to have no growth defect when grown alone, but can not compete with isogenic wild-type cells when grown in mixed culture [Basturea06].

Locations: cytosol

Map Position: [3,089,156 -> 3,089,887] (66.58 centisomes, 240°)
Length: 732 bp / 243 aa

Molecular Weight of Polypeptide: 26.978 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009665, EchoBASE:EB2269, EcoGene:EG12366, EcoliWiki:b2946, ModBase:P0AGL7, OU-Microarray:b2946, PortEco:rsmE, PR:PRO_000023885, Pride:P0AGL7, Protein Model Portal:P0AGL7, RefSeq:NP_417421, RegulonDB:EG12366, SMR:P0AGL7, String:511145.b2946, Swiss-Model:P0AGL7, UniProt:P0AGL7

Relationship Links: InterPro:IN-FAMILY:IPR006700, InterPro:IN-FAMILY:IPR015947, InterPro:IN-FAMILY:IPR029026, InterPro:IN-FAMILY:IPR029028, PDB:Structure:4E8B, Pfam:IN-FAMILY:PF04452

Gene-Reaction Schematic

Gene-Reaction Schematic

GO Terms:
Biological Process:
Inferred from experimentGO:0070475 - rRNA base methylation [Basturea06]
Inferred by computational analysisGO:0006364 - rRNA processing [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0032259 - methylation [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0070042 - rRNA (uridine-N3-)-methyltransferase activity [Basturea06]
Inferred by computational analysisGO:0008168 - methyltransferase activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a]
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: information transferRNA relatedRNA modification

Essentiality data for rsmE knockouts:

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

Created 23-Sep-2008 by Keseler I, SRI International
Last-Curated 23-Sep-2008 by Keseler I, SRI International

Enzymatic reaction of: 16S rRNA m3U1498 methyltransferase

Inferred from experiment

EC Number:

S-adenosyl-L-methionine + uracil1498 in 16S rRNA → S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA + H+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

The Km for 16S rRNA is measured as a Km for the physiological substrate, 30S ribosomal subunits [Basturea07].

Kinetic Parameters:
Substrate Km (μM) kcat (sec-1) kcat/Km (sec-1 μM-1) Citations
uracil1498 in 16S rRNA 2.0 0.0013 6.5e-4 [Basturea07, BRENDA14]
S-adenosyl-L-methionine 26.7, 26.7 7.0e-4 [Basturea07]

pH(opt): 7-9 [Basturea07]

Sequence Features

Protein sequence of 16S rRNA m3U1498 methyltransferase monomer with features indicated

Feature Class Location Citations Comment
Pfam PF04452 20 -> 236
Inferred by computational analysis[Finn14]
Methyltrans_RNA : RNA methyltransferase

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06].
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01].
10/20/97 Gene b2946 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12366; confirmed by SwissProt match.


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

Basturea06: Basturea GN, Rudd KE, Deutscher MP (2006). "Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family." RNA 12(3);426-34. PMID: 16431987

Basturea07: Basturea GN, Deutscher MP (2007). "Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE." RNA 13(11);1969-76. PMID: 17872509

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

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

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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