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Protein

23S rRNA (uracil-C(5))-methyltransferase RlmCD

Gene

rlmCD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the formation of 5-methyl-uridine at positions 747 (m5U747) and 1939 (m5U1939) in 23S rRNA.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + uracil(747) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(747) in 23S rRNA.1 Publication
S-adenosyl-L-methionine + uracil(1939) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S rRNA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi77 – 771Iron-sulfur (4Fe-4S)By similarity
Metal bindingi83 – 831Iron-sulfur (4Fe-4S)By similarity
Metal bindingi86 – 861Iron-sulfur (4Fe-4S)By similarity
Metal bindingi166 – 1661Iron-sulfur (4Fe-4S)By similarity
Binding sitei290 – 2901S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei319 – 3191S-adenosyl-L-methionine; via carbonyl oxygenPROSITE-ProRule annotation
Binding sitei340 – 3401S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei388 – 3881S-adenosyl-L-methioninePROSITE-ProRule annotation
Active sitei415 – 4151NucleophilePROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

  • rRNA methylation Source: UniProtKB
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

BioCyciBSUB:BSU06730-MONOMER.
BRENDAi2.1.1.189. 658.

Names & Taxonomyi

Protein namesi
Recommended name:
23S rRNA (uracil-C(5))-methyltransferase RlmCD (EC:2.1.1.189, EC:2.1.1.190)
Alternative name(s):
23S rRNA (uracil(1939)-C(5))-methyltransferase
23S rRNA (uracil(747)-C(5))-methyltransferase
Gene namesi
Name:rlmCD
Synonyms:yefA, yerS
Ordered Locus Names:BSU06730
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 45945923S rRNA (uracil-C(5))-methyltransferase RlmCDPRO_0000161953Add
BLAST

Proteomic databases

PaxDbiO31503.

Interactioni

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003798.

Structurei

3D structure databases

ProteinModelPortaliO31503.
SMRiO31503. Positions 1-455.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 6459TRAMPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105BZT. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000029867.
InParanoidiO31503.
KOiK03215.
OMAiWGEEYIY.
PhylomeDBiO31503.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 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.

O31503-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKMKPPVEKN EYYDVTFEDL THEGAGVAKV QGFPIFVPNA LPEEKAQIKV
60 70 80 90 100
TRVKKGFAFG RLIELKEESP HRTDAPCPIY KQCGGCQLQH MTYEGQLLFK
110 120 130 140 150
QKQVKDVLER IGKLDLSKVT VHPTLGMEDP WNYRNKAQVP VGEREGGLVA
160 170 180 190 200
GFYQQRSHDI IDMSACLIQQ SKNDEAVQAV KDICANYGVK AYNEERHKGW
210 220 230 240 250
LRHIMVRYGV VTGEMMIVFI TRTSDFPHKA KIIEDITAQF PHVKSIVQNI
260 270 280 290 300
NPNKTNVIFG NETNVIWGEE YIYDLIGDVK FAISARSFYQ VNPEQTKVLY
310 320 330 340 350
DKALEYAELQ GEETVIDAYC GIGTISLFLA KQAKKVYGVE IVPEAIEDAK
360 370 380 390 400
RNAELNGNTN AEFAVGEAET VIPKWYEEGI TADTLVVDPP RKGCDEALLR
410 420 430 440 450
TIVEMKPKRV VYVSCNPGTL ARDLRVLEDG GYVTREVQPV DMFPHTNHVE

CCVLIKLKE
Length:459
Mass (Da):51,819
Last modified:January 1, 1998 - v1
Checksum:i35E99547779421D5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL009126 Genomic DNA. Translation: CAB12493.1.
PIRiE69793.
RefSeqiNP_388555.1. NC_000964.3.
WP_003233892.1. NZ_JNCM01000032.1.

Genome annotation databases

EnsemblBacteriaiCAB12493; CAB12493; BSU06730.
GeneIDi936060.
KEGGibsu:BSU06730.
PATRICi18972992. VBIBacSub10457_0710.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL009126 Genomic DNA. Translation: CAB12493.1.
PIRiE69793.
RefSeqiNP_388555.1. NC_000964.3.
WP_003233892.1. NZ_JNCM01000032.1.

3D structure databases

ProteinModelPortaliO31503.
SMRiO31503. Positions 1-455.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100003798.

Proteomic databases

PaxDbiO31503.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12493; CAB12493; BSU06730.
GeneIDi936060.
KEGGibsu:BSU06730.
PATRICi18972992. VBIBacSub10457_0710.

Phylogenomic databases

eggNOGiENOG4105BZT. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000029867.
InParanoidiO31503.
KOiK03215.
OMAiWGEEYIY.
PhylomeDBiO31503.

Enzyme and pathway databases

BioCyciBSUB:BSU06730-MONOMER.
BRENDAi2.1.1.189. 658.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 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 nameiRLMCD_BACSU
AccessioniPrimary (citable) accession number: O31503
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: January 1, 1998
Last modified: September 7, 2016
This is version 97 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

Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. 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.