Ribosomal RNA large subunit methyltransferase M - Escherichia coli (strain K12)

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P0ADR6 (RLMM_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 64. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:	rlmM
Synonyms:	ygdE
Ordered Locus Names:	b2806, JW2777
ORF Names:	b1976

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	366 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.4 Ref.5 Ref.6 Ref.7
Catalytic activity	S-adenosyl-L-methionine + cytidine(2498) in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine(2498) in 23S rRNA. Ref.6 Ref.7
Subunit structure	Monomer. Ref.7
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01551.
Domain	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. Ref.7
Sequence similarities	Belongs to the methyltransferase superfamily. RlmE family. RlmM subfamily.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm
Ligand	S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	enzyme-directed rRNA 2'-O-methylation Inferred from mutant phenotype Ref.6. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	rRNA (cytosine-2'-O-)-methyltransferase activity Inferred from direct assay Ref.6. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 366

366

Ribosomal RNA large subunit methyltransferase M HAMAP-Rule MF_01551

PRO_0000070402

Regions

Region

221 – 224

S-adenosyl-L-methionine binding HAMAP-Rule MF_01551

Sites

Active site

306

Proton acceptor Probable

Binding site

188

S-adenosyl-L-methionine

Binding site

240

S-adenosyl-L-methionine

Binding site

260

S-adenosyl-L-methionine

Binding site

277

S-adenosyl-L-methionine

Secondary structure

366

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0ADR6 [UniParc].

Last modified December 6, 2005. Version 1.
Checksum: 595EE105DFB03677
Show »

FASTA

366

41,905

        10         20         30         40         50         60 
MNKVVLLCRP GFEKECAAEI TDKAGQREIF GFARVKENAG YVIYECYQPD DGDKLIRELP 

        70         80         90        100        110        120 
FSSLIFARQW FVVGELLQHL PPEDRITPIV GMLQGVVEKG GELRVEVADT NESKELLKFC 

       130        140        150        160        170        180 
RKFTVPLRAA LRDAGVLANY ETPKRPVVHV FFIAPGCCYT GYSYSNNNSP FYMGIPRLKF 

       190        200        210        220        230        240 
PADAPSRSTL KLEEAFHVFI PADEWDERLA NGMWAVDLGA CPGGWTYQLV KRNMWVYSVD 

       250        260        270        280        290        300 
NGPMAQSLMD TGQVTWLRED GFKFRPTRSN ISWMVCDMVE KPAKVAALMA QWLVNGWCRE 

       310        320        330        340        350        360 
TIFNLKLPMK KRYEEVSHNL AYIQAQLDEH GINAQIQARQ LYHDREEVTV HVRRIWAAVG 


GRRDER

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"GcvA, a LysR-type transcriptional regulator protein, activates expression of the cloned Citrobacter freundii ampC beta-lactamase gene in Escherichia coli: cross-talk between DNA-binding proteins." Everett M.J., Walsh T., Guay G., Bennett P.M. Microbiology 141:419-430(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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.
[4]	"Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs." Bujnicki J.M., Rychlewski L. Acta Microbiol. Pol. 49:253-260(2000) [PubMed] [Europe PMC] [Abstract] Cited for: PUTATIVE FUNCTION AS METHYLTRANSFERASE.
[5]	"Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases." Feder M., Pas J., Wyrwicz L.S., Bujnicki J.M. Gene 302:129-138(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PUTATIVE FUNCTION AS METHYLTRANSFERASE.
[6]	"YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA." Purta E., O'Connor M., Bujnicki J.M., Douthwaite S. Mol. Microbiol. 72:1147-1158(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A METHYLTRANSFERASE, CATALYTIC ACTIVITY.
[7]	"Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA." Punekar A.S., Shepherd T.R., Liljeruhm J., Forster A.C., Selmer M. Nucleic Acids Res. 40:10507-10520(2012) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOPENZYME AND IN COMPLEX WITH S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, DOMAIN, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X73413 Genomic DNA. Translation: CAA51815.1.
U29581 Genomic DNA. Translation: AAB40456.1.
U00096 Genomic DNA. Translation: AAC75848.1.
AP009048 Genomic DNA. Translation: BAE76878.1.

PIR

I41067.

RefSeq

NP_417286.1. NC_000913.2.
YP_491014.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4ATN	X-ray	1.95	A	1-366	[»]
4AUK	X-ray	1.90	A/B	1-366	[»]
4B17	X-ray	2.60	A	1-366	[»]

ProteinModelPortal

P0ADR6.

SMR

P0ADR6. Positions 1-357.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0ADR6. 14 interactions.

STRING

511145.b2806.

Proteomic databases

PaxDb

P0ADR6.

PRIDE

P0ADR6.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75848; AAC75848; b2806.
BAE76878; BAE76878; BAE76878.

GeneID

12934543.
947283.

KEGG

ecj:Y75_p2743.
eco:b2806.

PATRIC

32121028. VBIEscCol129921_2906.

Organism-specific databases

EchoBASE

EB1742.

EcoGene

EG11794. rlmM.

Phylogenomic databases

eggNOG

COG2933.

HOGENOM

HOG000247137.

K06968.

OMA

VIFECYQ.

ProtClustDB

PRK11760.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11794-MONOMER.
ECOL316407:JW2777-MONOMER.
MetaCyc:EG11794-MONOMER.

Gene expression databases

Genevestigator

P0ADR6.

Family and domain databases

HAMAP

MF_01551. 23SrRNA_methyltr_M.

InterPro

IPR002877. rRNA_MeTrfase_FtsJ_dom.
IPR011224. rRNA_MeTrfase_M.
[Graphical view]

Pfam

PF01728. FtsJ. 1 hit.
[Graphical view]

PIRSF

PIRSF028774. UCP028774. 1 hit.

ProtoNet

Search...

Entry information

Entry name

RLMM_ECOLI

Accession

Primary (citable) accession number: P0ADR6
Secondary accession number(s): P32066, Q2MA28

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 6, 2005
Last sequence update:	December 6, 2005
Last modified:	May 1, 2013
This is version 64 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents