Escherichia coli K-12 substr. MG1655 Enzyme: 23S rRNA m3Ψ1915 methyltransferase

Gene: rlmH Accession Numbers: EG11254 (EcoCyc), b0636, ECK0629

Synonyms: ybeA

Regulation Summary Diagram: ?

Regulation summary diagram for rlmH

Subunit composition of 23S rRNA m3Ψ1915 methyltransferase = [RlmH]2
         23S rRNA m3Ψ1915 methyltransferase = RlmH

RlmH is a methyltransferase that catalyzes the addition of a methyl group in the N3 position of the pseudouridine (Ψ) residue at nucleotide 1915 in 23S rRNA [Purta08, Ero08]. The enzyme requires the intact ribosome and the presence of pseudouridine at position 1915 in 23S rRNA for activity [Ero08, Ero10]. m3Ψ1915 is the only currently known methylated pseudouridine residue in bacterial RNAs.

Computational docking between RlmH and the ribosome shows contacts with both ribosomal subunits [Purta08], consistent with the requirement for intact ribosomes for in vitro activity [Ero08].

RlmH is a member of the SPOUT superfamily of methyltransferases [Anantharaman02, Tkaczuk07] and belongs to the α/β knot superfamily of proteins [Mallam07, Tkaczuk07]. Thermodynamic and kinetic analysis of folding of RlmH shows that the protein folds via a simple three-state sequential mechanism [Mallam07]. Folding may involve a slipknot intermediate [Sulkowska09]. The RlmH polypeptide chain has a trefoil knot conformation even in the denatured state [Mallam10]. Backbone NMR assignments for urea-denatured RlmH have been reported [Hsieh13]. RlmH is a dimer in solution [Purta06, Mallam07, Mallam10].

RlmH activity is influenced by the presence of specific nucleotides in stem-loop 69 (H69) surrounding Ψ1915 in 23S RNA [Leppik12].

An rlmH deletion mutant lacks the m3Ψ1915 modification [Purta08, Ero08] and has a slightly lower growth rate than wild type [Purta08].

RlmH: "rRNA large subunit methyltransferase H" [Purta08, Ero08]

Citations: [Sergiev12]

Locations: cytosol

Map Position: [667,471 <- 667,938] (14.39 centisomes, 52°)
Length: 468 bp / 155 aa

Molecular Weight of Polypeptide: 17.341 kD (from nucleotide sequence)

Molecular Weight of Multimer: 36.8 kD (experimental) [Mallam07]

Unification Links: ASAP:ABE-0002180 , DIP:DIP-11357N , EchoBASE:EB1234 , EcoGene:EG11254 , EcoliWiki:b0636 , Mint:MINT-1251153 , ModBase:P0A8I8 , OU-Microarray:b0636 , PortEco:rlmH , PR:PRO_000023770 , Pride:P0A8I8 , Protein Model Portal:P0A8I8 , RefSeq:NP_415169 , RegulonDB:EG11254 , SMR:P0A8I8 , String:511145.b0636 , UniProt:P0A8I8

Relationship Links: InterPro:IN-FAMILY:IPR003742 , InterPro:IN-FAMILY:IPR016051 , InterPro:IN-FAMILY:IPR029026 , InterPro:IN-FAMILY:IPR029028 , PDB:Structure:1NS5 , Pfam:IN-FAMILY:PF02590

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0031167 - rRNA methylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Purta08, Ero08]
GO:0070475 - rRNA base methylation Inferred from experiment [Ero08, Purta08]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0042803 - protein homodimerization activity Author statement Inferred from experiment [Mallam10, Purta08]
GO:0070038 - rRNA (pseudouridine-N3-)-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, Ero08, Purta08]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0043022 - ribosome binding Author statement [Purta08]
Cellular Component: GO:0005737 - cytoplasm Inferred by curator Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01, Purta08]

MultiFun Terms: information transfer RNA related RNA modification

Created 07-Sep-2006 by Keseler I , SRI International
Last-Curated ? 12-Jul-2013 by Keseler I , SRI International

Enzymatic reaction of: 23S rRNA m3Ψ1915 methyltransferase

EC Number:

S-adenosyl-L-methionine + a pseudouridine1915 in 23S rRNA <=> S-adenosyl-L-homocysteine + an N3-methylpseudouridine1915 in 23S rRNA + 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.

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
a pseudouridine1915 in 23S rRNA

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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 b0636 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11254; confirmed by SwissProt match.


Anantharaman02: Anantharaman V, Koonin EV, Aravind L (2002). "SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases." J Mol Microbiol Biotechnol 4(1);71-5. PMID: 11763972

Ero08: Ero R, Peil L, Liiv A, Remme J (2008). "Identification of pseudouridine methyltransferase in Escherichia coli." RNA 14(10):2223-33. PMID: 18755836

Ero10: Ero R, Leppik M, Liiv A, Remme J (2010). "Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD." RNA 16(11);2075-84. PMID: 20817755

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."

Hsieh13: Hsieh SJ, Mallam AL, Jackson SE, Hsu ST (2013). "Backbone NMR assignments of a topologically knotted protein in urea-denatured state." Biomol NMR Assign. PMID: 23821130

Leppik12: Leppik M, Ero R, Liiv A, Kipper K, Remme J (2012). "Different sensitivity of H69 modification enzymes RluD and RlmH to mutations in Escherichia coli 23S rRNA." Biochimie 94(5);1080-9. PMID: 22586702

Mallam07: Mallam AL, Jackson SE (2007). "A comparison of the folding of two knotted proteins: YbeA and YibK." J Mol Biol 366(2);650-65. PMID: 17169371

Mallam10: Mallam AL, Rogers JM, Jackson SE (2010). "Experimental detection of knotted conformations in denatured proteins." Proc Natl Acad Sci U S A 107(18);8189-94. PMID: 20393125

Purta06: Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM (2006). "The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase." BMC Mol Biol 7(1);23. PMID: 16848900

Purta08: Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S (2008). "YbeA is the m3{Psi} methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA." RNA 14(10):2234-44. PMID: 18755835

Sergiev12: Sergiev PV, Golovina AY, Sergeeva OV, Osterman IA, Nesterchuk MV, Bogdanov AA, Dontsova OA (2012). "How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?." Nucleic Acids Res 40(12);5694-705. PMID: 22411911

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

Sulkowska09: Sulkowska JI, Sulkowski P, Onuchic J (2009). "Dodging the crisis of folding proteins with knots." Proc Natl Acad Sci U S A 106(9);3119-24. PMID: 19211785

Tkaczuk07: Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM (2007). "Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases." BMC Bioinformatics 8;73. PMID: 17338813

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."

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

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 19.0 on Wed Oct 7, 2015, biocyc14.