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Protein

23S rRNA (uracil(747)-C(5))-methyltransferase RlmC

Gene

rlmC

Organism
Shewanella frigidimarina (strain NCIMB 400)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the formation of 5-methyl-uridine at position 747 (m5U747) in 23S rRNA.UniRule annotation

Catalytic activityi

S-adenosyl-L-methionine + uracil(747) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(747) in 23S rRNA.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi3 – 31Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi11 – 111Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi14 – 141Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi87 – 871Iron-sulfur (4Fe-4S)UniRule annotation
Binding sitei212 – 2121S-adenosyl-L-methionineUniRule annotation
Binding sitei241 – 2411S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation
Binding sitei262 – 2621S-adenosyl-L-methionineUniRule annotation
Binding sitei309 – 3091S-adenosyl-L-methionineUniRule annotation
Active sitei336 – 3361NucleophileUniRule annotation

GO - Molecular functioni

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

BioCyciSFRI318167:GIXS-603-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
23S rRNA (uracil(747)-C(5))-methyltransferase RlmCUniRule annotation (EC:2.1.1.189UniRule annotation)
Alternative name(s):
23S rRNA(m5U747)-methyltransferaseUniRule annotation
Gene namesi
Name:rlmCUniRule annotation
Synonyms:rumB
Ordered Locus Names:Sfri_0579
OrganismiShewanella frigidimarina (strain NCIMB 400)
Taxonomic identifieri318167 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
Proteomesi
  • UP000000684 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 37737723S rRNA (uracil(747)-C(5))-methyltransferase RlmCPRO_0000282013Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi318167.Sfri_0579.

Structurei

3D structure databases

ProteinModelPortaliQ087X5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmC subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107SFS. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000218547.
KOiK03212.
OMAiNIQPIHM.
OrthoDBiEOG6V4GKM.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01012. 23SrRNA_methyltr_RlmC.
InterProiIPR011825. 23SrRNA_MeTrfase_RlmC.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR029063. SAM-dependent_MTases.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR02085. meth_trns_rumB. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q087X5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKCDYFERGD CLSCRNIQLP MVEQVSVKQQ QLIDLFRGIS VKQWLAPILS
60 70 80 90 100
AESGFRNKAK MVVLGAAHKP ILGLVNPKGE PVSLCDCSLY PKDMQLLLHR
110 120 130 140 150
LERFVQQAGI PPYRVDKSKG ELKFILLTRS QSSGQFMLRF VLRSDQAIVR
160 170 180 190 200
IERELPQLLQ EFPEITLVSA NIQPIHMAIL EGEREIFLTE TTRLEEQLNN
210 220 230 240 250
VPLFIRPKSF FQTNPEVAAQ LYQIAREWVT EFKPNYIWDL FCGVGGFGLH
260 270 280 290 300
CADSNIRLTG IEIESEAIEC AILSATKLGF TQVDFSALDS THFAKGQSAQ
310 320 330 340 350
DKPDLIIVNP PRRGLGKSLC DSLSEFAPKA IVYSSCNPHT LMSDLEYITG
360 370
YQITKVQMFD MFPHTDHFEV LVMLEQL
Length:377
Mass (Da):42,746
Last modified:October 31, 2006 - v1
Checksum:i541E7AFCA916D3D9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000447 Genomic DNA. Translation: ABI70440.1.
RefSeqiWP_011636067.1. NC_008345.1.

Genome annotation databases

EnsemblBacteriaiABI70440; ABI70440; Sfri_0579.
KEGGisfr:Sfri_0579.
PATRICi23494949. VBISheFri14343_0599.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000447 Genomic DNA. Translation: ABI70440.1.
RefSeqiWP_011636067.1. NC_008345.1.

3D structure databases

ProteinModelPortaliQ087X5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi318167.Sfri_0579.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABI70440; ABI70440; Sfri_0579.
KEGGisfr:Sfri_0579.
PATRICi23494949. VBISheFri14343_0599.

Phylogenomic databases

eggNOGiENOG4107SFS. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000218547.
KOiK03212.
OMAiNIQPIHM.
OrthoDBiEOG6V4GKM.

Enzyme and pathway databases

BioCyciSFRI318167:GIXS-603-MONOMER.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01012. 23SrRNA_methyltr_RlmC.
InterProiIPR011825. 23SrRNA_MeTrfase_RlmC.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR029063. SAM-dependent_MTases.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR02085. meth_trns_rumB. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NCIMB 400.

Entry informationi

Entry nameiRLMC_SHEFN
AccessioniPrimary (citable) accession number: Q087X5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: October 31, 2006
Last modified: November 11, 2015
This is version 60 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. 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.