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Protein

Ribosomal RNA large subunit methyltransferase M

Gene

rlmM

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

Functioni

Catalyzes the 2'-O-methylation at nucleotide C2498 in 23S rRNA. Modifies C2498 in naked 23S rRNA, but not in assembled 50S subunits or ribosomes.2 Publications

Catalytic activityi

S-adenosyl-L-methionine + cytidine(2498) in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine(2498) in 23S rRNA.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei188 – 1881S-adenosyl-L-methionine1 Publication
Binding sitei240 – 2401S-adenosyl-L-methionine1 Publication
Binding sitei260 – 2601S-adenosyl-L-methionine1 Publication
Binding sitei277 – 2771S-adenosyl-L-methionine1 Publication
Active sitei306 – 3061Proton acceptor1 Publication

GO - Molecular functioni

  • rRNA (cytosine-2'-O-)-methyltransferase activity Source: EcoCyc

GO - Biological processi

  • enzyme-directed rRNA 2'-O-methylation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG11794-MONOMER.
ECOL316407:JW2777-MONOMER.
MetaCyc:EG11794-MONOMER.
BRENDAi2.1.1.186. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA large subunit methyltransferase M (EC:2.1.1.186)
Alternative name(s):
23S rRNA (cytidine2498-2'-O)-methyltransferase
23S rRNA 2'-O-ribose methyltransferase RlmM
Gene namesi
Name:rlmM
Synonyms:ygdE
Ordered Locus Names:b2806, JW2777
ORF Names:b1976
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11794. rlmM.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 366366Ribosomal RNA large subunit methyltransferase MPRO_0000070402Add
BLAST

Proteomic databases

PaxDbiP0ADR6.
PRIDEiP0ADR6.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4263537. 17 interactions.
IntActiP0ADR6. 14 interactions.
STRINGi511145.b2806.

Structurei

Secondary structure

1
366
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75Combined sources
Helixi13 – 2614Combined sources
Beta strandi31 – 344Combined sources
Beta strandi40 – 489Combined sources
Helixi51 – 588Combined sources
Helixi61 – 633Combined sources
Beta strandi68 – 736Combined sources
Helixi86 – 938Combined sources
Turni94 – 963Combined sources
Beta strandi99 – 1068Combined sources
Beta strandi109 – 1113Combined sources
Helixi114 – 13320Combined sources
Beta strandi147 – 1548Combined sources
Beta strandi157 – 1637Combined sources
Helixi172 – 1743Combined sources
Helixi189 – 19911Combined sources
Helixi202 – 2043Combined sources
Helixi205 – 2084Combined sources
Beta strandi214 – 2185Combined sources
Helixi224 – 2318Combined sources
Beta strandi235 – 2395Combined sources
Helixi246 – 2494Combined sources
Turni250 – 2523Combined sources
Beta strandi254 – 2574Combined sources
Turni261 – 2633Combined sources
Beta strandi271 – 2766Combined sources
Helixi282 – 29413Combined sources
Beta strandi299 – 3068Combined sources
Beta strandi309 – 3113Combined sources
Helixi312 – 32918Combined sources
Beta strandi334 – 3396Combined sources
Beta strandi345 – 35410Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4ATNX-ray1.95A1-366[»]
4AUKX-ray1.90A/B1-366[»]
4B17X-ray2.60A1-366[»]
ProteinModelPortaliP0ADR6.
SMRiP0ADR6. Positions 1-357.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni221 – 2244S-adenosyl-L-methionine binding

Domaini

Consists of two structural domains: an N-terminal THUMP domain followed by a C-terminal catalytic Rossmann-like fold MTase domain in a novel arrangement. The two domains are connected by a long loop.1 Publication

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105EZ6. Bacteria.
COG2933. LUCA.
HOGENOMiHOG000247137.
InParanoidiP0ADR6.
KOiK06968.
OMAiVIFECYQ.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01551. 23SrRNA_methyltr_M. 1 hit.
InterProiIPR002877. rRNA_MeTrfase_FtsJ_dom.
IPR011224. rRNA_MeTrfase_M.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01728. FtsJ. 1 hit.
[Graphical view]
PIRSFiPIRSF028774. UCP028774. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.

Sequencei

Sequence statusi: Complete.

P0ADR6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNKVVLLCRP GFEKECAAEI TDKAGQREIF GFARVKENAG YVIYECYQPD
60 70 80 90 100
DGDKLIRELP FSSLIFARQW FVVGELLQHL PPEDRITPIV GMLQGVVEKG
110 120 130 140 150
GELRVEVADT NESKELLKFC RKFTVPLRAA LRDAGVLANY ETPKRPVVHV
160 170 180 190 200
FFIAPGCCYT GYSYSNNNSP FYMGIPRLKF PADAPSRSTL KLEEAFHVFI
210 220 230 240 250
PADEWDERLA NGMWAVDLGA CPGGWTYQLV KRNMWVYSVD NGPMAQSLMD
260 270 280 290 300
TGQVTWLRED GFKFRPTRSN ISWMVCDMVE KPAKVAALMA QWLVNGWCRE
310 320 330 340 350
TIFNLKLPMK KRYEEVSHNL AYIQAQLDEH GINAQIQARQ LYHDREEVTV
360
HVRRIWAAVG GRRDER
Length:366
Mass (Da):41,905
Last modified:December 6, 2005 - v1
Checksum:i595EE105DFB03677
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X73413 Genomic DNA. Translation: CAA51815.1.
U29581 Genomic DNA. Translation: AAB40456.1.
U00096 Genomic DNA. Translation: AAC75848.1.
AP009048 Genomic DNA. Translation: BAE76878.1.
PIRiI41067.
RefSeqiNP_417286.1. NC_000913.3.
WP_001045520.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75848; AAC75848; b2806.
BAE76878; BAE76878; BAE76878.
GeneIDi947283.
KEGGiecj:JW2777.
eco:b2806.
PATRICi32121028. VBIEscCol129921_2906.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X73413 Genomic DNA. Translation: CAA51815.1.
U29581 Genomic DNA. Translation: AAB40456.1.
U00096 Genomic DNA. Translation: AAC75848.1.
AP009048 Genomic DNA. Translation: BAE76878.1.
PIRiI41067.
RefSeqiNP_417286.1. NC_000913.3.
WP_001045520.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4ATNX-ray1.95A1-366[»]
4AUKX-ray1.90A/B1-366[»]
4B17X-ray2.60A1-366[»]
ProteinModelPortaliP0ADR6.
SMRiP0ADR6. Positions 1-357.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263537. 17 interactions.
IntActiP0ADR6. 14 interactions.
STRINGi511145.b2806.

Proteomic databases

PaxDbiP0ADR6.
PRIDEiP0ADR6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75848; AAC75848; b2806.
BAE76878; BAE76878; BAE76878.
GeneIDi947283.
KEGGiecj:JW2777.
eco:b2806.
PATRICi32121028. VBIEscCol129921_2906.

Organism-specific databases

EchoBASEiEB1742.
EcoGeneiEG11794. rlmM.

Phylogenomic databases

eggNOGiENOG4105EZ6. Bacteria.
COG2933. LUCA.
HOGENOMiHOG000247137.
InParanoidiP0ADR6.
KOiK06968.
OMAiVIFECYQ.

Enzyme and pathway databases

BioCyciEcoCyc:EG11794-MONOMER.
ECOL316407:JW2777-MONOMER.
MetaCyc:EG11794-MONOMER.
BRENDAi2.1.1.186. 2026.

Miscellaneous databases

PROiP0ADR6.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01551. 23SrRNA_methyltr_M. 1 hit.
InterProiIPR002877. rRNA_MeTrfase_FtsJ_dom.
IPR011224. rRNA_MeTrfase_M.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01728. FtsJ. 1 hit.
[Graphical view]
PIRSFiPIRSF028774. UCP028774. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRLMM_ECOLI
AccessioniPrimary (citable) accession number: P0ADR6
Secondary accession number(s): P32066, Q2MA28
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: December 6, 2005
Last modified: September 7, 2016
This is version 84 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.