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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)DescriptionActionsGraphical viewLength
Metal bindingi81Iron-sulfur (4Fe-4S)2 Publications1
Metal bindingi87Iron-sulfur (4Fe-4S)2 Publications1
Metal bindingi90Iron-sulfur (4Fe-4S)2 Publications1
Metal bindingi162Iron-sulfur (4Fe-4S)2 Publications1
Binding sitei265S-adenosyl-L-methionine1 Publication1
Binding sitei294S-adenosyl-L-methionine; via carbonyl oxygen1 Publication1
Binding sitei299S-adenosyl-L-methionine1 Publication1
Binding sitei315S-adenosyl-L-methionine1 Publication1
Binding sitei342S-adenosyl-L-methionine1 Publication1
Binding sitei363S-adenosyl-L-methionine1 Publication1
Active sitei389NucleophileUniRule annotation1 Publication1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11247. rlmD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001618932 – 43323S rRNA (uracil(1939)-C(5))-methyltransferase RlmDAdd BLAST432

Proteomic databases

PaxDbiP55135.
PRIDEiP55135.

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei132Interaction with RNA1
Sitei149Interaction with RNA1

Protein-protein interaction databases

BioGridi4262285. 11 interactors.
DIPiDIP-12119N.
IntActiP55135. 1 interactor.
STRINGi511145.b2785.

Structurei

Secondary structure

1433
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi17 – 24Combined sources8
Beta strandi28 – 34Combined sources7
Beta strandi37 – 42Combined sources6
Beta strandi49 – 57Combined sources9
Beta strandi59 – 69Combined sources11
Turni82 – 86Combined sources5
Beta strandi87 – 89Combined sources3
Helixi97 – 112Combined sources16
Beta strandi118 – 120Combined sources3
Beta strandi124 – 126Combined sources3
Beta strandi128 – 138Combined sources11
Turni139 – 142Combined sources4
Beta strandi143 – 150Combined sources8
Beta strandi156 – 158Combined sources3
Helixi167 – 180Combined sources14
Helixi184 – 188Combined sources5
Beta strandi189 – 197Combined sources9
Beta strandi200 – 209Combined sources10
Helixi213 – 226Combined sources14
Beta strandi229 – 237Combined sources9
Beta strandi240 – 243Combined sources4
Beta strandi248 – 251Combined sources4
Beta strandi254 – 257Combined sources4
Beta strandi260 – 262Combined sources3
Helixi268 – 282Combined sources15
Beta strandi289 – 294Combined sources6
Turni296 – 300Combined sources5
Helixi301 – 305Combined sources5
Beta strandi308 – 316Combined sources9
Helixi318 – 330Combined sources13
Beta strandi335 – 340Combined sources6
Beta strandi348 – 350Combined sources3
Helixi351 – 353Combined sources3
Beta strandi358 – 362Combined sources5
Helixi370 – 379Combined sources10
Beta strandi382 – 389Combined sources8
Helixi391 – 403Combined sources13
Beta strandi407 – 414Combined sources8
Beta strandi424 – 430Combined sources7

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP55135.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini10 – 68TRAMUniRule annotationAdd BLAST59

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni23 – 40Interaction with RNAAdd BLAST18
Regioni58 – 63Interaction with RNA6

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.
PhylomeDBiP55135.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UWVX-ray1.95A1-433[»]
2BH2X-ray2.15A/B2-433[»]
ProteinModelPortaliP55135.
SMRiP55135.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262285. 11 interactors.
DIPiDIP-12119N.
IntActiP55135. 1 interactor.
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.
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

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD. 1 hit.
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...

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: November 2, 2016
This is version 137 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.