Escherichia coli K-12 substr. MG1655 Enzyme: 23S rRNA m5U1939 methyltransferase

Gene: rlmD Accession Numbers: EG11247 (EcoCyc), b2785, ECK2779

Synonyms: ygcA, rumA

Regulation Summary Diagram: ?

Regulation summary diagram for rlmD

RlmD is the methyltransferase responsible for methylation of 23S rRNA at the C5 position of the U1939 nucleotide [Agarwalla02, Madsen03]. In vitro, the enzyme methylates full-length 23S rRNA as well as a 70 nt fragment containing nucleotides 1930-1969 [Agarwalla02].

Crystal structures of apo-RlmD and a ternary complex have been solved at 1.95 and 2.15 Å resolution, suggesting active site residues and a mechanism for base selectivity [Lee04b, Lee05g]. Since methyltransferase reactions do not involve a redox step, the presence of a [4Fe-4S] iron-sulfur cluster was unexpected. The iron-sulfur cluster was hypothesized to provide a mechanism for regulating RlmD activity under oxidative stress conditions [Agarwalla04].

RumA: RNA uridine methyltransferase [Agarwalla02]

Review: [Hur06]

Locations: cytosol

Map Position: [2,911,721 <- 2,913,022] (62.76 centisomes, 226°)
Length: 1302 bp / 433 aa

Molecular Weight of Polypeptide: 48.052 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009127 , DIP:DIP-12119N , EchoBASE:EB1228 , EcoGene:EG11247 , EcoliWiki:b2785 , ModBase:P55135 , OU-Microarray:b2785 , PortEco:rlmD , PR:PRO_000023895 , Pride:P55135 , Protein Model Portal:P55135 , RefSeq:NP_417265 , RegulonDB:EG11247 , SMR:P55135 , String:511145.b2785 , UniProt:P55135

Relationship Links: InterPro:IN-FAMILY:IPR001566 , InterPro:IN-FAMILY:IPR002792 , InterPro:IN-FAMILY:IPR010280 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR029063 , InterPro:IN-FAMILY:IPR030390 , InterPro:IN-FAMILY:IPR030391 , PDB:Structure:1UWV , PDB:Structure:2BH2 , Pfam:IN-FAMILY:PF01938 , Pfam:IN-FAMILY:PF05958 , Prosite:IN-FAMILY:PS01230 , Prosite:IN-FAMILY:PS01231 , Prosite:IN-FAMILY:PS50926 , Prosite:IN-FAMILY:PS51687

In Paralogous Gene Group: 217 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0070475 - rRNA base methylation Inferred from experiment [Agarwalla02]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01]
GO:0031167 - rRNA methylation Inferred by computational analysis [GOA06]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Agarwalla04]
GO:0070041 - rRNA (uridine-C5-)-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, Agarwalla02]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA06]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11]
GO:0008173 - RNA methyltransferase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rlmD 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]

Last-Curated ? 18-Sep-2008 by Keseler I , SRI International

Enzymatic reaction of: 23S rRNA m5U1939 methyltransferase

EC Number:

a uracil1939 in 23S rRNA + S-adenosyl-L-methionine <=> a 5-methyluracil1939 in 23S rRNA + S-adenosyl-L-homocysteine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Agarwalla02, Lee04b]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Agarwalla02, BRENDA14]

Sequence Features

Protein sequence of 23S rRNA m5U1939 methyltransferase with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Agarwalla02, UniProt11]
UniProt: Removed.
Chain 2 -> 433
UniProt: 23S rRNA (uracil-5-)-methyltransferase rumA;
Conserved-Region 10 -> 68
UniProt: TRAM;
Protein-Segment 23 -> 40
UniProt: Interaction with RNA; Sequence Annotation Type: region of interest;
Protein-Segment 58 -> 63
UniProt: Interaction with RNA; Sequence Annotation Type: region of interest;
Metal-Binding-Site 81
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 87
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 90
UniProt: Iron-sulfur (4Fe-4S).
Amino-Acid-Site 132
UniProt: Interaction with RNA; Sequence Annotation Type: site.
Amino-Acid-Site 149
UniProt: Interaction with RNA; Sequence Annotation Type: site.
Metal-Binding-Site 162
UniProt: Iron-sulfur (4Fe-4S).
Amino-Acid-Sites-That-Bind 265
UniProt: S-adenosyl-L-methionine.
Amino-Acid-Sites-That-Bind 294
UniProt: S-adenosyl-L-methionine; via carbonyl oxygen.
Amino-Acid-Sites-That-Bind 299
UniProt: S-adenosyl-L-methionine.
Amino-Acid-Sites-That-Bind 315
UniProt: S-adenosyl-L-methionine.
Amino-Acid-Sites-That-Bind 342
UniProt: S-adenosyl-L-methionine.
Amino-Acid-Sites-That-Bind 363
UniProt: S-adenosyl-L-methionine.
Active-Site 389
[Lee05g, UniProt11]
UniProt: Nucleophile.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2785 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11247.


Agarwalla02: Agarwalla S, Kealey JT, Santi DV, Stroud RM (2002). "Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli." J Biol Chem 277(11);8835-40. PMID: 11779873

Agarwalla04: Agarwalla S, Stroud RM, Gaffney BJ (2004). "Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies." J Biol Chem 279(33);34123-9. PMID: 15181002

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

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

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hur06: Hur S, Stroud RM, Finer-Moore J (2006). "Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective." J Biol Chem 281(51);38969-73. PMID: 17085441

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

Lee04b: Lee TT, Agarwalla S, Stroud RM (2004). "Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase." Structure (Camb) 12(3);397-407. PMID: 15016356

Lee05g: Lee TT, Agarwalla S, Stroud RM (2005). "A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function." Cell 120(5);599-611. PMID: 15766524

Madsen03: Madsen CT, Mengel-Jorgensen J, Kirpekar F, Douthwaite S (2003). "Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry." Nucleic Acids Res 31(16);4738-46. PMID: 12907714

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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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 19.0 on Mon Oct 5, 2015, biocyc13.