|Gene:||rlmH||Accession Numbers: EG11254 (EcoCyc), b0636, ECK0629|
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.
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 [Hsieh13a]. 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].
|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
|Biological Process:||GO:0031167 - rRNA methylation
[GOA06, GOA01, Purta08, Ero08]
GO:0070475 - rRNA base methylation [Ero08, Purta08]
GO:0006364 - rRNA processing [UniProtGOA11, GOA01]
GO:0032259 - methylation [UniProtGOA11]
|Molecular Function:||GO:0042803 - protein homodimerization activity
GO:0070038 - rRNA (pseudouridine-N3-)-methyltransferase activity [GOA06, Ero08, Purta08]
GO:0008168 - methyltransferase activity [UniProtGOA11, GOA01]
GO:0016740 - transferase activity [UniProtGOA11]
GO:0043022 - ribosome binding [Purta08]
|Cellular Component:||GO:0005737 - cytoplasm [UniProtGOA11a, UniProtGOA11, GOA06, GOA01, Purta08]|
|MultiFun Terms:||information transfer → RNA related → RNA modification|
Enzymatic reaction of: 23S rRNA m3Ψ1915 methyltransferase
EC Number: 220.127.116.11
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.
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
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
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
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
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
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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