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P55135 (RLMD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 115. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
EC=2.1.1.190
Alternative name(s):
23S rRNA(m5U1939)-methyltransferase
Gene names
Name:rlmD
Synonyms:rumA, ygcA
Ordered Locus Names:b2785, JW2756
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length433 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA. Ref.3 Ref.4

Catalytic activity

S-adenosyl-L-methionine + uracil(1939) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S rRNA. Ref.3 Ref.4

Domain

Contains three structural domains: an N-terminal TRAM domain, a central domain containing an iron-sulfur cluster, and a C-terminal domain that displays the typical SAM-dependent methyltransferase fold. HAMAP-Rule MF_01010

Miscellaneous

The function of the iron-sulfur cluster remains unclear. It may be involved in the correct folding of the protein or may have a role in RNA binding. HAMAP-Rule MF_01010

Sequence similarities

Belongs to the methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily.

Contains 1 TRAM domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.3
Chain2 – 43343223S rRNA (uracil(1939)-C(5))-methyltransferase RlmD HAMAP-Rule MF_01010
PRO_0000161893

Regions

Domain10 – 6859TRAM
Region23 – 4018Interaction with RNA HAMAP-Rule MF_01010
Region58 – 636Interaction with RNA HAMAP-Rule MF_01010

Sites

Active site3891Nucleophile Ref.6
Metal binding811Iron-sulfur (4Fe-4S)
Metal binding871Iron-sulfur (4Fe-4S)
Metal binding901Iron-sulfur (4Fe-4S)
Metal binding1621Iron-sulfur (4Fe-4S)
Binding site2651S-adenosyl-L-methionine
Binding site2941S-adenosyl-L-methionine; via carbonyl oxygen
Binding site2991S-adenosyl-L-methionine
Binding site3151S-adenosyl-L-methionine
Binding site3421S-adenosyl-L-methionine
Binding site3631S-adenosyl-L-methionine
Site1321Interaction with RNA
Site1491Interaction with RNA

Secondary structure

1 ......................................................................... 433
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P55135 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: A46C07B0BD18EAAC

FASTA43348,052
        10         20         30         40         50         60 
MAQFYSAKRR TTTRQIITVS VNDLDSFGQG VARHNGKTLF IPGLLPQENA EVTVTEDKKQ 

        70         80         90        100        110        120 
YARAKVVRRL SDSPERETPR CPHFGVCGGC QQQHASVDLQ QRSKSAALAR LMKHDVSEVI 

       130        140        150        160        170        180 
ADVPWGYRRR ARLSLNYLPK TQQLQMGFRK AGSSDIVDVK QCPILAPQLE ALLPKVRACL 

       190        200        210        220        230        240 
GSLQAMRHLG HVELVQATSG TLMILRHTAP LSSADREKLE RFSHSEGLDL YLAPDSEILE 

       250        260        270        280        290        300 
TVSGEMPWYD SNGLRLTFSP RDFIQVNAGV NQKMVARALE WLDVQPEDRV LDLFCGMGNF 

       310        320        330        340        350        360 
TLPLATQAAS VVGVEGVPAL VEKGQQNARL NGLQNVTFYH ENLEEDVTKQ PWAKNGFDKV 

       370        380        390        400        410        420 
LLDPARAGAA GVMQQIIKLE PIRIVYVSCN PATLARDSEA LLKAGYTIAR LAMLDMFPHT 

       430 
GHLESMVLFS RVK

« Hide

References

« Hide 'large scale' references
[1]"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.
[2]"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.
[3]"Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli."
Agarwalla S., Kealey J.T., Santi D.V., Stroud R.M.
J. Biol. Chem. 277:8835-8840(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, CHARACTERIZATION.
[4]"Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry."
Madsen C.T., Mengel-Joergensen J., Kirpekar F., Douthwaite S.
Nucleic Acids Res. 31:4738-4746(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY.
[5]"Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase."
Lee T.T., Agarwalla S., Stroud R.M.
Structure 12:397-407(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 15-431, IRON-SULFUR CLUSTER.
[6]"A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function."
Lee T.T., Agarwalla S., Stroud R.M.
Cell 120:599-611(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH RNA; S-ADENOSYL-L-HOMOCYSTEINE AND IRON-SULFUR CLUSTER, ACTIVE SITE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		U29580 Genomic DNA. Translation: AAA69295.1.
U00096 Genomic DNA. Translation: AAC75827.1.
AP009048 Genomic DNA. Translation: BAE76859.1.
PIRE65060.
RefSeqNP_417265.1. NC_000913.2.
YP_490993.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1UWVX-ray1.95A1-433[»]
2BH2X-ray2.15A/B1-433[»]
ProteinModelPortalP55135.
SMRP55135. Positions 15-431.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-12119N.
IntActP55135. 1 interaction.
STRING511145.b2785.

Proteomic databases

PRIDEP55135.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75827; AAC75827; b2785.
BAE76859; BAE76859; BAE76859.
GeneID12933291.
947243.
KEGGecj:Y75_p2722.
eco:b2785.
PATRIC32120986. VBIEscCol129921_2885.

Organism-specific databases

EchoBASEEB1228.
EcoGeneEG11247. rlmD.

Phylogenomic databases

eggNOGCOG2265.
HOGENOMHOG000029868.
KOK03215.
OMAHNGAGIA.
ProtClustDBPRK13168.

Enzyme and pathway databases

BioCycEcoCyc:EG11247-MONOMER.
ECOL316407:JW2756-MONOMER.
MetaCyc:EG11247-MONOMER.

Gene expression databases

GenevestigatorP55135.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
HAMAPMF_01010. 23SrRNA_methyltr_RlmD.
InterProIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR012340. NA-bd_OB-fold.
IPR002792. TRAM_dom.
IPR010280. U5_MeTrfase.
[Graphical view]
PfamPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMSSF50249. Nucleic_acid_OB. 1 hit.
TIGRFAMsTIGR00479. rumA. 1 hit.
PROSITEPS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP55135.

Entry information

Entry nameRLMD_ECOLI
AccessionPrimary (citable) accession number: P55135
Secondary accession number(s): Q2MA47
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: May 1, 2013
This is version 115 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic 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

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents