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Protein

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

Gene

rlmC

Organism
Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6)
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 sitei307 – 3071S-adenosyl-L-methionineUniRule annotation
Active sitei334 – 3341NucleophileUniRule 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

BioCyciXNEM406817:GHY4-1537-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
Ordered Locus Names:XNC1_1533
OrganismiXenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6)
Taxonomic identifieri406817 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeXenorhabdus
Proteomesi
  • UP000008075 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 37537523S rRNA (uracil(747)-C(5))-methyltransferase RlmCPRO_0000414826Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi406817.XNC1_1533.

Structurei

3D structure databases

ProteinModelPortaliD3VBF7.
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.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01012. 23SrRNA_methyltr_RlmC.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR011825. 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.
TIGR00479. rumA. 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.

D3VBF7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQCVQYTAGH CHSCQWLDKS YSHQLSDKQK HLKQLLQETS VTHWLSPVMS
60 70 80 90 100
KTSGFRNKAK MVVNGSVERP LLGMLHRDGR TVDLCDCPLY PQHFQAVFEV
110 120 130 140 150
IKVFIAKAGL VPYNVERRKG ELKYILLTES RANNEMMLRF VLRSETKLAQ
160 170 180 190 200
LERVLPWLQE QLPQLTVISA NIQPTHMAIL EGEKEIIFTG QTMLKETFNG
210 220 230 240 250
IPLYIRPRSF FQTNPDIASE LYATAGRWVR ELNISSMWDL FCGAGGFGLH
260 270 280 290 300
CADKETKLTG IEISAEAIDC AKSSAKSLGL KSVEFQALDS THFALEKAKI
310 320 330 340 350
PELVLVNPPR RGIGKELCEY LSRMAPKFVL YSSCNAETMA KDIAMLKQYR
360 370
IEKVQLFDMF PHTEHYETLA LLILD
Length:375
Mass (Da):42,662
Last modified:April 20, 2010 - v1
Checksum:i0606B17AE1D0A7A3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FN667742 Genomic DNA. Translation: CBJ89596.1.
RefSeqiWP_013183906.1. NC_014228.1.

Genome annotation databases

EnsemblBacteriaiCBJ89596; CBJ89596; XNC1_1533.
GeneIDi24902197.
KEGGixne:XNC1_1533.
PATRICi42462880. VBIXenNem38452_1414.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FN667742 Genomic DNA. Translation: CBJ89596.1.
RefSeqiWP_013183906.1. NC_014228.1.

3D structure databases

ProteinModelPortaliD3VBF7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi406817.XNC1_1533.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCBJ89596; CBJ89596; XNC1_1533.
GeneIDi24902197.
KEGGixne:XNC1_1533.
PATRICi42462880. VBIXenNem38452_1414.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyciXNEM406817:GHY4-1537-MONOMER.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01012. 23SrRNA_methyltr_RlmC.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR011825. 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.
TIGR00479. rumA. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete genome sequence of Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6)."
    Goodrich-Blair H., Barbazuk B., Bode H.B., Darby C., Du Z., Forst S., Gaudriault S., Goldman B.S., Goodner B., Henkhaus J., Latreille P., Medigue C., Miller N., Norton S., Ogier J.C., Rouy Z., Slater S., Suen G.
    Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6.

Entry informationi

Entry nameiRLMC_XENNA
AccessioniPrimary (citable) accession number: D3VBF7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 25, 2012
Last sequence update: April 20, 2010
Last modified: November 11, 2015
This is version 38 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.