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Protein

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

Gene

rlmD

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

Functioni

Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA.UniRule annotation2 Publications

Catalytic activityi

S-adenosyl-L-methionine + uracil(1939) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S rRNA.UniRule annotation2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi81 – 811Iron-sulfur (4Fe-4S)2 Publications
Metal bindingi87 – 871Iron-sulfur (4Fe-4S)2 Publications
Metal bindingi90 – 901Iron-sulfur (4Fe-4S)2 Publications
Metal bindingi162 – 1621Iron-sulfur (4Fe-4S)2 Publications
Binding sitei265 – 2651S-adenosyl-L-methionine1 Publication
Binding sitei294 – 2941S-adenosyl-L-methionine; via carbonyl oxygen1 Publication
Binding sitei299 – 2991S-adenosyl-L-methionine1 Publication
Binding sitei315 – 3151S-adenosyl-L-methionine1 Publication
Binding sitei342 – 3421S-adenosyl-L-methionine1 Publication
Binding sitei363 – 3631S-adenosyl-L-methionine1 Publication
Active sitei389 – 3891NucleophileUniRule annotation1 Publication

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: EcoCyc
  • iron ion binding Source: UniProtKB-HAMAP
  • RNA binding Source: InterPro
  • rRNA (uridine-C5-)-methyltransferase activity Source: EcoCyc

GO - Biological processi

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

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG11247-MONOMER.
ECOL316407:JW2756-MONOMER.
MetaCyc:EG11247-MONOMER.
BRENDAi2.1.1.190. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmDUniRule annotation (EC:2.1.1.190UniRule annotation)
Alternative name(s):
23S rRNA(m5U1939)-methyltransferaseUniRule annotation
Gene namesi
Name:rlmDUniRule annotation
Synonyms:rumA, ygcA
Ordered Locus Names:b2785, JW2756
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11247. rlmD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 43343223S rRNA (uracil(1939)-C(5))-methyltransferase RlmDPRO_0000161893Add
BLAST

Proteomic databases

PaxDbiP55135.
PRIDEiP55135.

Interactioni

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei132 – 1321Interaction with RNA
Sitei149 – 1491Interaction with RNA

Protein-protein interaction databases

BioGridi4262285. 11 interactions.
DIPiDIP-12119N.
IntActiP55135. 1 interaction.
STRINGi511145.b2785.

Structurei

Secondary structure

1
433
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi17 – 248Combined sources
Beta strandi28 – 347Combined sources
Beta strandi37 – 426Combined sources
Beta strandi49 – 579Combined sources
Beta strandi59 – 6911Combined sources
Turni82 – 865Combined sources
Beta strandi87 – 893Combined sources
Helixi97 – 11216Combined sources
Beta strandi118 – 1203Combined sources
Beta strandi124 – 1263Combined sources
Beta strandi128 – 13811Combined sources
Turni139 – 1424Combined sources
Beta strandi143 – 1508Combined sources
Beta strandi156 – 1583Combined sources
Helixi167 – 18014Combined sources
Helixi184 – 1885Combined sources
Beta strandi189 – 1979Combined sources
Beta strandi200 – 20910Combined sources
Helixi213 – 22614Combined sources
Beta strandi229 – 2379Combined sources
Beta strandi240 – 2434Combined sources
Beta strandi248 – 2514Combined sources
Beta strandi254 – 2574Combined sources
Beta strandi260 – 2623Combined sources
Helixi268 – 28215Combined sources
Beta strandi289 – 2946Combined sources
Turni296 – 3005Combined sources
Helixi301 – 3055Combined sources
Beta strandi308 – 3169Combined sources
Helixi318 – 33013Combined sources
Beta strandi335 – 3406Combined sources
Beta strandi348 – 3503Combined sources
Helixi351 – 3533Combined sources
Beta strandi358 – 3625Combined sources
Helixi370 – 37910Combined sources
Beta strandi382 – 3898Combined sources
Helixi391 – 40313Combined sources
Beta strandi407 – 4148Combined sources
Beta strandi424 – 4307Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UWVX-ray1.95A1-433[»]
2BH2X-ray2.15A/B2-433[»]
ProteinModelPortaliP55135.
SMRiP55135. Positions 15-431.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP55135.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini10 – 6859TRAMUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni23 – 4018Interaction with RNAAdd
BLAST
Regioni58 – 636Interaction with RNA

Domaini

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.1 Publication

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily.UniRule annotation
Contains 1 TRAM domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105BZT. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000029868.
InParanoidiP55135.
KOiK03215.
OMAiDLDPFGQ.
OrthoDBiEOG6V4GKM.
PhylomeDBiP55135.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases.
IPR002792. TRAM_dom.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00479. rumA. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P55135-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQFYSAKRR TTTRQIITVS VNDLDSFGQG VARHNGKTLF IPGLLPQENA
60 70 80 90 100
EVTVTEDKKQ YARAKVVRRL SDSPERETPR CPHFGVCGGC QQQHASVDLQ
110 120 130 140 150
QRSKSAALAR LMKHDVSEVI ADVPWGYRRR ARLSLNYLPK TQQLQMGFRK
160 170 180 190 200
AGSSDIVDVK QCPILAPQLE ALLPKVRACL GSLQAMRHLG HVELVQATSG
210 220 230 240 250
TLMILRHTAP LSSADREKLE RFSHSEGLDL YLAPDSEILE TVSGEMPWYD
260 270 280 290 300
SNGLRLTFSP RDFIQVNAGV NQKMVARALE WLDVQPEDRV LDLFCGMGNF
310 320 330 340 350
TLPLATQAAS VVGVEGVPAL VEKGQQNARL NGLQNVTFYH ENLEEDVTKQ
360 370 380 390 400
PWAKNGFDKV LLDPARAGAA GVMQQIIKLE PIRIVYVSCN PATLARDSEA
410 420 430
LLKAGYTIAR LAMLDMFPHT GHLESMVLFS RVK
Length:433
Mass (Da):48,052
Last modified:January 23, 2007 - v3
Checksum:iA46C07B0BD18EAAC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29580 Genomic DNA. Translation: AAA69295.1.
U00096 Genomic DNA. Translation: AAC75827.1.
AP009048 Genomic DNA. Translation: BAE76859.1.
PIRiE65060.
RefSeqiNP_417265.1. NC_000913.3.
WP_000046812.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75827; AAC75827; b2785.
BAE76859; BAE76859; BAE76859.
GeneIDi947243.
KEGGiecj:JW2756.
eco:b2785.
PATRICi32120986. VBIEscCol129921_2885.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29580 Genomic DNA. Translation: AAA69295.1.
U00096 Genomic DNA. Translation: AAC75827.1.
AP009048 Genomic DNA. Translation: BAE76859.1.
PIRiE65060.
RefSeqiNP_417265.1. NC_000913.3.
WP_000046812.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UWVX-ray1.95A1-433[»]
2BH2X-ray2.15A/B2-433[»]
ProteinModelPortaliP55135.
SMRiP55135. Positions 15-431.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262285. 11 interactions.
DIPiDIP-12119N.
IntActiP55135. 1 interaction.
STRINGi511145.b2785.

Proteomic databases

PaxDbiP55135.
PRIDEiP55135.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75827; AAC75827; b2785.
BAE76859; BAE76859; BAE76859.
GeneIDi947243.
KEGGiecj:JW2756.
eco:b2785.
PATRICi32120986. VBIEscCol129921_2885.

Organism-specific databases

EchoBASEiEB1228.
EcoGeneiEG11247. rlmD.

Phylogenomic databases

eggNOGiENOG4105BZT. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000029868.
InParanoidiP55135.
KOiK03215.
OMAiDLDPFGQ.
OrthoDBiEOG6V4GKM.
PhylomeDBiP55135.

Enzyme and pathway databases

BioCyciEcoCyc:EG11247-MONOMER.
ECOL316407:JW2756-MONOMER.
MetaCyc:EG11247-MONOMER.
BRENDAi2.1.1.190. 2026.

Miscellaneous databases

EvolutionaryTraceiP55135.
PROiP55135.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases.
IPR002792. TRAM_dom.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00479. rumA. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. 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, DOMAIN.
  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.

Entry informationi

Entry nameiRLMD_ECOLI
AccessioniPrimary (citable) accession number: P55135
Secondary accession number(s): Q2MA47
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: January 20, 2016
This is version 134 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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.