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Protein

RNA-splicing ligase RtcB

Gene

rtcB

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

Functioni

RNA ligase that mediates the joining of broken tRNA-like stem-loop structures in case of tRNA damage. Probably participates to tRNA restriction-repair by ligating broken tRNA-like stem-loop structures with 2',3'-cyclic phosphate and 5'-OH ends to form a splice junction with a 2'-OH, 3',5'-phosphodiester, a step that requires GTP (PubMed:21224389, PubMed:22730297). Also acts as a DNA ligase in case of DNA damage by splicing 'dirty' DNA breaks, characterized by 3'-PO4 (or cyclic-PO4) and 5'-OH ends that cannot be sealed by classical DNA ligases (PubMed:24218597).6 Publications

Miscellaneous

In contrast to the vertebrate homolog, ligation does not seem to require ATP, while GTP stimulates activity.1 Publication
Ligation proceeds through 3 nucleotidyl transfer steps, with 2',3'-cyclic phosphate termini being hydrolyzed to 3'-P termini in a step that precedes 3'-P activation with GMP. In the first nucleotidyl transfer step, RtcB reacts with GTP to form a covalent RtcB-histidine-GMP intermediate with release of PPi; in the second step, the GMP moiety is transferred to the RNA 3'-P; in the third step, the 5'-OH from the opposite RNA strand attacks the activated 3'-P to form a 3',5'-phosphodiester bond and release GMP (PubMed:22474365). Acts as a DNA ligase by attaching a GMP nucleotide to the DNA 3'-PO4 end to activate it for nucleophilic attack by the 5'-OH (PubMed:24218597).2 Publications

Cofactori

Mn2+2 PublicationsNote: Binds 2 manganese ions per subunit.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi75Manganese 1By similarity1
Metal bindingi78Manganese 1By similarity1
Metal bindingi78Manganese 2By similarity1
Metal bindingi168Manganese 1By similarity1
Binding sitei171GMPBy similarity1
Metal bindingi185Manganese 2By similarity1
Metal bindingi281Manganese 2By similarity1
Binding sitei320GMPBy similarity1
Active sitei337GMP-histidine intermediate1 Publication1
Binding sitei407GMPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi281 – 282GMPBy similarity2
Nucleotide bindingi311 – 314GMPBy similarity4
Nucleotide bindingi337 – 340GMPBy similarity4

GO - Molecular functioni

  • DNA ligase activity Source: EcoCyc
  • manganese ion binding Source: UniProtKB
  • RNA ligase activity Source: EcoCyc

GO - Biological processi

  • cellular response to DNA damage stimulus Source: UniProtKB
  • DNA repair Source: UniProtKB
  • RNA processing Source: UniProtKB
  • RNA repair Source: EcoCyc

Keywordsi

Molecular functionLigase
Biological processDNA damage, DNA repair
LigandManganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7751-MONOMER
MetaCyc:G7751-MONOMER
BRENDAi6.5.1.4 2026

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-splicing ligase RtcB (EC:6.5.1.-)
Gene namesi
Name:rtcB
Synonyms:yhgL
Ordered Locus Names:b3421, JW3384
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12939 rtcB

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi337H → A, N or Q: Loss of function. Abolishes formation of guanylylated RtcB intermediate. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002151091 – 408RNA-splicing ligase RtcBAdd BLAST408

Proteomic databases

PaxDbiP46850
PRIDEiP46850

2D gel databases

SWISS-2DPAGEP46850

Expressioni

Inductioni

Expression is repressed by RtcR.1 Publication

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4261188, 7 interactors
IntActiP46850, 20 interactors
STRINGi316385.ECDH10B_3595

Structurei

3D structure databases

ProteinModelPortaliP46850
SMRiP46850
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RtcB family.Curated

Phylogenomic databases

eggNOGiENOG4105E0Y Bacteria
COG1690 LUCA
HOGENOMiHOG000220066
InParanoidiP46850
KOiK14415
OMAiYDVAHNV
PhylomeDBiP46850

Family and domain databases

Gene3Di3.90.1860.10, 1 hit
InterProiView protein in InterPro
IPR001233 RtcB
IPR036025 RtcB-like_sf
PfamiView protein in Pfam
PF01139 RtcB, 1 hit
SUPFAMiSSF103365 SSF103365, 1 hit
PROSITEiView protein in PROSITE
PS01288 UPF0027, 1 hit

Sequencei

Sequence statusi: Complete.

P46850-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNYELLTTEN APVKMWTKGV PVEADARQQL INTAKMPFIF KHIAVMPDVH
60 70 80 90 100
LGKGSTIGSV IPTKGAIIPA AVGVDIGCGM NALRTALTAE DLPENLAELR
110 120 130 140 150
QAIETAVPHG RTTGRCKRDK GAWENPPVNV DAKWAELEAG YQWLTQKYPR
160 170 180 190 200
FLNTNNYKHL GTLGTGNHFI EICLDESDQV WIMLHSGSRG IGNAIGTYFI
210 220 230 240 250
DLAQKEMQET LETLPSRDLA YFMEGTEYFD DYLKAVAWAQ LFASLNRDAM
260 270 280 290 300
MENVVTALQS ITQKTVRQPQ TLAMEEINCH HNYVQKEQHF GEEIYVTRKG
310 320 330 340 350
AVSARAGQYG IIPGSMGAKS FIVRGLGNEE SFCSCSHGAG RVMSRTKAKK
360 370 380 390 400
LFSVEDQIRA TAHVECRKDA EVIDEIPMAY KDIDAVMAAQ SDLVEVIYTL

RQVVCVKG
Length:408
Mass (Da):45,222
Last modified:July 15, 1998 - v3
Checksum:iC0C33BA04542185F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti84R → G in AAA58219 (PubMed:9278503).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA Translation: AAA58219.1
U00096 Genomic DNA Translation: AAC76446.1
AP009048 Genomic DNA Translation: BAE77871.1
PIRiH65137
RefSeqiNP_417879.1, NC_000913.3
WP_001105504.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC76446; AAC76446; b3421
BAE77871; BAE77871; BAE77871
GeneIDi947929
KEGGiecj:JW3384
eco:b3421
PATRICifig|511145.12.peg.3516

Similar proteinsi

Entry informationi

Entry nameiRTCB_ECOLI
AccessioniPrimary (citable) accession number: P46850
Secondary accession number(s): P76690, Q2M785
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: July 15, 1998
Last modified: March 28, 2018
This is version 107 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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