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Escherichia coli K-12 substr. MG1655 Enzyme: 23S rRNA 2'-O-ribose U2552 methyltransferase



Gene: rlmE Accession Numbers: EG11507 (EcoCyc), b3179, ECK3168

Synonyms: ftsJ, mrsF, rrmJ, ribosomal RNA large subunit methyltransferase E

Regulation Summary Diagram: ?

Summary:
RlmE is the methyltransferase responsible for methylation of 23S rRNA at the 2'-O position of the ribose at the universally conserved U2552 nucleotide [Caldas00]. In vitro, the enzyme is active on ribosomes and the 50S ribosomal subunit, but not free rRNA [Caldas00, Bugl00].

A crystal structure of RlmE has been solved at 1.5 Å resolution [Bugl00]. Site-directed mutagenesis has identified possible active site and substrate binding residues, and a reaction mechanism has been proposed [Hager02, Hager04].

A mutant strain lacking RlmE has a decreased growth rate at all temperatures tested and shows reduced protein synthesis activity and accumulation of free ribosomal subunits [Caldas00a, Bugl00]. Overexpression of the small GTPases Obg, Der [Tan02, Hwang10a] or CtgA [Jiang06a] suppresses the ribosomal assembly or stability defect of an rlmE mutant without restoring the methylation of U2552 [Tan02]. An rlmE-deficient strain shows a decrease in -1 and +1 frameshifting and a decrease in UAA and UGA stop codon readthrough, suggesting that the U2552 base may interact with aminoacyl-tRNAs at the ribosomal A site [Widerak05].

An rlmE mutant is more sensitive to lincomycin [Caldas00a], clindamycin, hygromycin A and sparsomycin [Toh08] than wild-type.

Gene Citations: [Tomoyasu93, Herman95]

Locations: cytosol

Map Position: [3,325,057 <- 3,325,686] (71.67 centisomes)
Length: 630 bp / 209 aa

Molecular Weight of Polypeptide: 23.335 kD (from nucleotide sequence), 23.0 kD (experimental) [Caldas00 ]

Unification Links: ASAP:ABE-0010447 , CGSC:33511 , DIP:DIP-47902N , EchoBASE:EB1470 , EcoGene:EG11507 , EcoliWiki:b3179 , EcoO157Cyc:FTSJ-MONOMER , Mint:MINT-1257637 , ModBase:P0C0R7 , OU-Microarray:b3179 , PortEco:rlmE , PR:PRO_000023767 , Pride:P0C0R7 , Protein Model Portal:P0C0R7 , RefSeq:NP_417646 , RegulonDB:EG11507 , SMR:P0C0R7 , String:511145.b3179 , Swiss-Model:P0C0R7 , UniProt:P0C0R7

Relationship Links: InterPro:IN-FAMILY:IPR002877 , InterPro:IN-FAMILY:IPR004512 , InterPro:IN-FAMILY:IPR015507 , Panther:IN-FAMILY:PTHR10920 , PDB:Structure:1EIZ , PDB:Structure:1EJ0 , Pfam:IN-FAMILY:PF01728

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000453 - enzyme-directed rRNA 2'-O-methylation Inferred from experiment [Caldas00]
GO:0001510 - RNA methylation Inferred by computational analysis [GOA01]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0008650 - rRNA (uridine-2'-O-)-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, Caldas00]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016436 - rRNA (uridine) 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 computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rlmE 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:
Last-Curated ? 18-Sep-2008 by Keseler I , SRI International


Enzymatic reaction of: 23S rRNA 2'-O-ribose U2552 methyltransferase

EC Number: 2.1.1.166

uridine2552 in 23S rRNA + S-adenosyl-L-methionine <=> 2-O-methyluridine2552 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 of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
uridine2552 in 23S rRNA
0.8
[Hager02]
S-adenosyl-L-methionine
3.7
0.001
[Hager02, BRENDA14]

T(opt): 55 °C [BRENDA14, Hager02]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 20
[Hager04, UniProt11]
Alternate sequence: D → A; UniProt: 2-fold decrease in activity. Increase in Km for 50S subunit.
Mutagenesis-Variant 22
[Hager04, UniProt11]
Alternate sequence: Y → A; UniProt: No change in activity.
Mutagenesis-Variant 32
[Hager04, UniProt11]
Alternate sequence: R → A; UniProt: 4-fold decrease in activity and increase in Km for 50S subunit; when associated with A-34.
Mutagenesis-Variant 34
[Hager04, UniProt11]
Alternate sequence: R → A; UniProt: 4-fold decrease in activity and increase in Km for 50S subunit; when associated with A-32.
Mutagenesis-Variant 38
[Hager02, UniProt11]
Alternate sequence: K → A; UniProt: Loss of activity. Almost no change in S-adenosyl-L-methionine binding.
Amino-Acid-Sites-That-Bind 63
[UniProt10a]
UniProt: S-adenosyl-L-methionine; via amide nitrogen;
Amino-Acid-Sites-That-Bind 65
[UniProt10a]
UniProt: S-adenosyl-L-methionine; via amide nitrogen;
Mutagenesis-Variant 83
[Hager02, UniProt11]
Alternate sequence: D → A; UniProt: 5-fold decrease in activity. Increase in Km for 50S subunit and for S- adenosyl-L-methionine. Loss of S- adenosyl-L-methionine binding.
Amino-Acid-Sites-That-Bind 83
[UniProt10a]
UniProt: S-adenosyl-L-methionine;
Amino-Acid-Sites-That-Bind 99
[UniProt10a]
UniProt: S-adenosyl-L-methionine;
Mutagenesis-Variant 124
[Hager02, UniProt11]
Alternate sequence: D → A; UniProt: Loss of activity. Loss of S- adenosyl-L-methionine binding.
Amino-Acid-Sites-That-Bind 124
[UniProt10a]
UniProt: S-adenosyl-L-methionine;
Mutagenesis-Variant 136
[Hager04, UniProt11]
Alternate sequence: D → N; UniProt: 2-fold decrease in activity.
Mutagenesis-Variant 164
[Hager02, UniProt11]
Alternate sequence: K → A; UniProt: Loss of activity. No change in S- adenosyl-L-methionine binding.
Active-Site 164
[Hager02, UniProt11]
UniProt: Proton acceptor.
Mutagenesis-Variant 189
[Hager04, UniProt11]
Alternate sequence: K → A; UniProt: 9-fold decrease in activity.
Mutagenesis-Variant 194
[Hager04, UniProt11]
Alternate sequence: R → A; UniProt: No change in activity. Increase in Km for 50S subunit.
Mutagenesis-Variant 197
[Hager04, UniProt11]
Alternate sequence: S → A; UniProt: No change in activity. Increase in Km for 50S subunit.
Mutagenesis-Variant 199
[Hager02, UniProt11]
Alternate sequence: E → A; UniProt: 16-fold decrease in activity. No change in S-adenosyl-L-methionine binding.
Mutagenesis-Variant 201
[Hager02, UniProt11]
Alternate sequence: Y → A; UniProt: 5-fold decrease in activity. Almost no change in S-adenosyl-L-methionine binding.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3179 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11507; confirmed by SwissProt match.


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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Bugl00: Bugl H, Fauman EB, Staker BL, Zheng F, Kushner SR, Saper MA, Bardwell JC, Jakob U (2000). "RNA methylation under heat shock control." Mol Cell 6(2);349-60. PMID: 10983982

Caldas00: Caldas T, Binet E, Bouloc P, Costa A, Desgres J, Richarme G (2000). "The FtsJ/RrmJ heat shock protein of Escherichia coli is a 23 S ribosomal RNA methyltransferase." J Biol Chem 275(22);16414-9. PMID: 10748051

Caldas00a: Caldas T, Binet E, Bouloc P, Richarme G (2000). "Translational defects of Escherichia coli mutants deficient in the Um(2552) 23S ribosomal RNA methyltransferase RrmJ/FTSJ." Biochem Biophys Res Commun 271(3);714-8. PMID: 10814528

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."

Hager02: Hager J, Staker BL, Bugl H, Jakob U (2002). "Active site in RrmJ, a heat shock-induced methyltransferase." J Biol Chem 277(44);41978-86. PMID: 12181314

Hager04: Hager J, Staker BL, Jakob U (2004). "Substrate binding analysis of the 23S rRNA methyltransferase RrmJ." J Bacteriol 186(19);6634-42. PMID: 15375145

Herman95: Herman C, Thevenet D, D'Ari R, Bouloc P (1995). "Degradation of sigma 32, the heat shock regulator in Escherichia coli, is governed by HflB." Proc Natl Acad Sci U S A 1995;92(8);3516-20. PMID: 7724592

Hwang10a: Hwang J, Inouye M (2010). "The interaction of an essential E. coli GTPase, Der with 50S ribosome via the KH-like domain." J Bacteriol 192(8):2277-83. PMID: 20172997

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

Jiang06a: Jiang M, Datta K, Walker A, Strahler J, Bagamasbad P, Andrews PC, Maddock JR (2006). "The Escherichia coli GTPase CgtAE Is Involved in Late Steps of Large Ribosome Assembly." J Bacteriol 188(19);6757-70. PMID: 16980477

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

Tan02: Tan J, Jakob U, Bardwell JC (2002). "Overexpression of two different GTPases rescues a null mutation in a heat-induced rRNA methyltransferase." J Bacteriol 184(10);2692-8. PMID: 11976298

Toh08: Toh SM, Mankin AS (2008). "An indigenous posttranscriptional modification in the ribosomal peptidyl transferase center confers resistance to an array of protein synthesis inhibitors." J Mol Biol 380(4);593-7. PMID: 18554609

Tomoyasu93: Tomoyasu T, Yuki T, Morimura S, Mori H, Yamanaka K, Niki H, Hiraga S, Ogura T (1993). "The Escherichia coli FtsH protein is a prokaryotic member of a protein family of putative ATPases involved in membrane functions, cell cycle control, and gene expression." J Bacteriol 1993;175(5);1344-51. PMID: 8444796

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: 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."

Widerak05: Widerak M, Kern R, Malki A, Richarme G (2005). "U2552 methylation at the ribosomal A-site is a negative modulator of translational accuracy." Gene 347(1);109-14. PMID: 15715963

Other References Related to Gene Regulation

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065


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 Fri Nov 21, 2014, BIOCYC14B.