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Protein

RNA-splicing ligase RtcB

Gene

rtcB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi75 – 751Manganese 1By similarity
Metal bindingi78 – 781Manganese 1By similarity
Metal bindingi78 – 781Manganese 2By similarity
Metal bindingi168 – 1681Manganese 1By similarity
Binding sitei171 – 1711GMPBy similarity
Metal bindingi185 – 1851Manganese 2By similarity
Metal bindingi281 – 2811Manganese 2By similarity
Binding sitei320 – 3201GMPBy similarity
Active sitei337 – 3371GMP-histidine intermediate1 Publication
Binding sitei407 – 4071GMPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi281 – 2822GMPBy similarity
Nucleotide bindingi311 – 3144GMPBy similarity
Nucleotide bindingi337 – 3404GMPBy similarity

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: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7751-MONOMER.
ECOL316407:JW3384-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12939. rtcB.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi337 – 3371H → A, N or Q: Loss of function. Abolishes formation of guanylylated RtcB intermediate. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 408408RNA-splicing ligase RtcBPRO_0000215109Add
BLAST

Proteomic databases

PaxDbiP46850.

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 interactions.
IntActiP46850. 20 interactions.
STRINGi511145.b3421.

Structurei

3D structure databases

ProteinModelPortaliP46850.
SMRiP46850. Positions 28-408.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RtcB family.Curated

Phylogenomic databases

eggNOGiENOG4105E0Y. Bacteria.
COG1690. LUCA.
HOGENOMiHOG000220066.
InParanoidiP46850.
KOiK14415.
OMAiYDVAHNV.
OrthoDBiEOG6F81M0.
PhylomeDBiP46850.

Family and domain databases

InterProiIPR001233. RtcB.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 1 hit.
PfamiPF01139. RtcB. 1 hit.
[Graphical view]
SUPFAMiSSF103365. SSF103365. 1 hit.
PROSITEiPS01288. UPF0027. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti84 – 841R → G in AAA58219 (PubMed:9278503).Curated

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.
PATRICi32122278. VBIEscCol129921_3516.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP46850.
SMRiP46850. Positions 28-408.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261188. 7 interactions.
IntActiP46850. 20 interactions.
STRINGi511145.b3421.

2D gel databases

SWISS-2DPAGEP46850.

Proteomic databases

PaxDbiP46850.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76446; AAC76446; b3421.
BAE77871; BAE77871; BAE77871.
GeneIDi947929.
KEGGiecj:JW3384.
eco:b3421.
PATRICi32122278. VBIEscCol129921_3516.

Organism-specific databases

EchoBASEiEB2774.
EcoGeneiEG12939. rtcB.

Phylogenomic databases

eggNOGiENOG4105E0Y. Bacteria.
COG1690. LUCA.
HOGENOMiHOG000220066.
InParanoidiP46850.
KOiK14415.
OMAiYDVAHNV.
OrthoDBiEOG6F81M0.
PhylomeDBiP46850.

Enzyme and pathway databases

BioCyciEcoCyc:G7751-MONOMER.
ECOL316407:JW3384-MONOMER.
MetaCyc:G7751-MONOMER.
BRENDAi6.5.1.4. 2026.

Miscellaneous databases

PROiP46850.

Family and domain databases

InterProiIPR001233. RtcB.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 1 hit.
PfamiPF01139. RtcB. 1 hit.
[Graphical view]
SUPFAMiSSF103365. SSF103365. 1 hit.
PROSITEiPS01288. UPF0027. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon."
    Genschik P., Drabikowski K., Filipowicz W.
    J. Biol. Chem. 273:25516-25526(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE NAME.
  4. "RtcB is the RNA ligase component of an Escherichia coli RNA repair operon."
    Tanaka N., Shuman S.
    J. Biol. Chem. 286:7727-7731(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, INDUCTION.
    Strain: K12.
  5. "RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo."
    Tanaka N., Meineke B., Shuman S.
    J. Biol. Chem. 286:30253-30257(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, COFACTOR.
  6. "Novel mechanism of RNA repair by RtcB via sequential 2',3'-cyclic phosphodiesterase and 3'-Phosphate/5'-hydroxyl ligation reactions."
    Tanaka N., Chakravarty A.K., Maughan B., Shuman S.
    J. Biol. Chem. 286:43134-43143(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, COFACTOR.
  7. "The sequential 2',3'-cyclic phosphodiesterase and 3'-phosphate/5'-OH ligation steps of the RtcB RNA splicing pathway are GTP-dependent."
    Chakravarty A.K., Shuman S.
    Nucleic Acids Res. 40:8558-8567(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-(histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates."
    Chakravarty A.K., Subbotin R., Chait B.T., Shuman S.
    Proc. Natl. Acad. Sci. U.S.A. 109:6072-6077(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, ACTIVE SITE, REACTION MECHANISM, MUTAGENESIS OF HIS-337.
  9. "Rewriting the rules for end joining via enzymatic splicing of DNA 3'-PO4 and 5'-OH ends."
    Das U., Chakravarty A.K., Remus B.S., Shuman S.
    Proc. Natl. Acad. Sci. U.S.A. 110:20437-20442(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, REACTION MECHANISM.

Entry informationi

Entry nameiRTCB_ECOLI
AccessioniPrimary (citable) accession number: P46850
Secondary accession number(s): P76690, Q2M785
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: July 15, 1998
Last modified: July 6, 2016
This is version 98 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  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.