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Protein

Ribosomal RNA large subunit methyltransferase H

Gene

rlmH

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. Specific for fully assembled 70S ribosomes.2 Publications

Catalytic activityi

S-adenosyl-L-methionine + pseudouridine(1915) in 23S rRNA = S-adenosyl-L-homocysteine + N(3)-methylpseudouridine(1915) in 23S rRNA.

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB
  • ribosome binding Source: UniProtKB
  • rRNA (pseudouridine-N3-)-methyltransferase activity Source: UniProtKB

GO - Biological processi

  • rRNA base methylation Source: EcoCyc
  • rRNA methylation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG11254-MONOMER.
ECOL316407:JW0631-MONOMER.
MetaCyc:EG11254-MONOMER.
BRENDAi2.1.1.177. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA large subunit methyltransferase H (EC:2.1.1.177)
Alternative name(s):
23S rRNA (pseudouridine1915-N3)-methyltransferase
23S rRNA m3Psi1915 methyltransferase
rRNA (pseudouridine-N3-)-methyltransferase RlmH
Gene namesi
Name:rlmH
Synonyms:ybeA
Ordered Locus Names:b0636, JW0631
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11254. rlmH.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 155155Ribosomal RNA large subunit methyltransferase HPRO_0000198115Add
BLAST

Proteomic databases

PaxDbiP0A8I8.
PRIDEiP0A8I8.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
rpsBP0A7V01EBI-560148,EBI-543439

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

DIPiDIP-11357N.
IntActiP0A8I8. 11 interactions.
MINTiMINT-1251153.
STRINGi511145.b0636.

Structurei

Secondary structure

1
155
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi14 – 2411Combined sources
Beta strandi33 – 386Combined sources
Helixi49 – 6416Combined sources
Beta strandi67 – 726Combined sources
Helixi81 – 9414Combined sources
Beta strandi98 – 1025Combined sources
Helixi110 – 1156Combined sources
Beta strandi117 – 1204Combined sources
Helixi129 – 14719Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NS5X-ray1.68A/B1-155[»]
ProteinModelPortaliP0A8I8.
SMRiP0A8I8. Positions 1-155.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8I8.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNA methyltransferase RlmH family.Curated

Phylogenomic databases

eggNOGiENOG4108UXA. Bacteria.
COG1576. LUCA.
HOGENOMiHOG000218434.
InParanoidiP0A8I8.
KOiK00783.
OMAiLGSYRDQ.
OrthoDBiEOG6S26HR.
PhylomeDBiP0A8I8.

Family and domain databases

Gene3Di3.40.1280.10. 1 hit.
HAMAPiMF_00658. 23SrRNA_methyltr_H.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR016051. RlmH.
IPR003742. SPOUT_MeTrfase.
IPR029026. tRNA_m1G_MTases_N.
[Graphical view]
PfamiPF02590. SPOUT_MTase. 1 hit.
[Graphical view]
PIRSFiPIRSF004505. MT_bac. 1 hit.
SUPFAMiSSF75217. SSF75217. 1 hit.
TIGRFAMsiTIGR00246. tRNA_RlmH_YbeA. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A8I8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLQLVAVGT KMPDWVQTGF TEYLRRFPKD MPFELIEIPA GKRGKNADIK
60 70 80 90 100
RILDKEGEQM LAAAGKNRIV TLDIPGKPWD TPQLAAELER WKLDGRDVSL
110 120 130 140 150
LIGGPEGLSP ACKAAAEQSW SLSALTLPHP LVRVLVAESL YRAWSITTNH

PYHRE
Length:155
Mass (Da):17,341
Last modified:June 7, 2005 - v1
Checksum:iDFA0EFCF4EB057E7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04516 Genomic DNA. Translation: CAA28200.1.
U82598 Genomic DNA. Translation: AAB40836.1.
U00096 Genomic DNA. Translation: AAC73737.1.
AP009048 Genomic DNA. Translation: BAA35283.1.
PIRiB24995. QQECP1.
RefSeqiNP_415169.1. NC_000913.3.
WP_000776104.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73737; AAC73737; b0636.
BAA35283; BAA35283; BAA35283.
GeneIDi945239.
KEGGiecj:JW0631.
eco:b0636.
PATRICi32116455. VBIEscCol129921_0667.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04516 Genomic DNA. Translation: CAA28200.1.
U82598 Genomic DNA. Translation: AAB40836.1.
U00096 Genomic DNA. Translation: AAC73737.1.
AP009048 Genomic DNA. Translation: BAA35283.1.
PIRiB24995. QQECP1.
RefSeqiNP_415169.1. NC_000913.3.
WP_000776104.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NS5X-ray1.68A/B1-155[»]
ProteinModelPortaliP0A8I8.
SMRiP0A8I8. Positions 1-155.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-11357N.
IntActiP0A8I8. 11 interactions.
MINTiMINT-1251153.
STRINGi511145.b0636.

Proteomic databases

PaxDbiP0A8I8.
PRIDEiP0A8I8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73737; AAC73737; b0636.
BAA35283; BAA35283; BAA35283.
GeneIDi945239.
KEGGiecj:JW0631.
eco:b0636.
PATRICi32116455. VBIEscCol129921_0667.

Organism-specific databases

EchoBASEiEB1234.
EcoGeneiEG11254. rlmH.

Phylogenomic databases

eggNOGiENOG4108UXA. Bacteria.
COG1576. LUCA.
HOGENOMiHOG000218434.
InParanoidiP0A8I8.
KOiK00783.
OMAiLGSYRDQ.
OrthoDBiEOG6S26HR.
PhylomeDBiP0A8I8.

Enzyme and pathway databases

BioCyciEcoCyc:EG11254-MONOMER.
ECOL316407:JW0631-MONOMER.
MetaCyc:EG11254-MONOMER.
BRENDAi2.1.1.177. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A8I8.
PROiP0A8I8.

Family and domain databases

Gene3Di3.40.1280.10. 1 hit.
HAMAPiMF_00658. 23SrRNA_methyltr_H.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR016051. RlmH.
IPR003742. SPOUT_MeTrfase.
IPR029026. tRNA_m1G_MTases_N.
[Graphical view]
PfamiPF02590. SPOUT_MTase. 1 hit.
[Graphical view]
PIRSFiPIRSF004505. MT_bac. 1 hit.
SUPFAMiSSF75217. SSF75217. 1 hit.
TIGRFAMsiTIGR00246. tRNA_RlmH_YbeA. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin-binding protein 2 of Escherichia coli K12."
    Asoh S., Matsuzawa H., Ishino F., Strominger J.L., Matsuhashi M., Ohta T.
    Eur. J. Biochem. 160:231-238(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Identification of pseudouridine methyltransferase in Escherichia coli."
    Ero R., Peil L., Liiv A., Remme J.
    RNA 14:2223-2233(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A METHYLTRANSFERASE, CATALYTIC ACTIVITY.
    Strain: K12 / MG1655 / ATCC 47076.
  7. "YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA."
    Purta E., Kaminska K.H., Kasprzak J.M., Bujnicki J.M., Douthwaite S.
    RNA 14:2234-2244(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A METHYLTRANSFERASE, CATALYTIC ACTIVITY, 3D-STRUCTURE MODELING.
  8. "Structure of ybeA from E.coli."
    Northeast structural genomics consortium (NESG)
    Submitted (JAN-2005) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiRLMH_ECOLI
AccessioniPrimary (citable) accession number: P0A8I8
Secondary accession number(s): P05850
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: November 11, 2015
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.