UniProtKB - P46850 (RTCB_ECOLI)
Protein
RNA-splicing ligase RtcB
Gene
rtcB
Organism
Escherichia coli (strain K12)
Status
Functioni
GTP-dependent RNA ligase that is involved in tRNA splicing and RNA repair (PubMed:21224389, PubMed:21757685, PubMed:22045815, PubMed:22730297, PubMed:22474365, PubMed:26858100). Joins RNA with 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy ends (PubMed:21224389, PubMed:21757685, PubMed:22045815, PubMed:22730297, PubMed:22474365, PubMed:26858100). Also acts as a DNA ligase in case of DNA damage by splicing 'dirty' DNA breaks, characterized by 3'-phosphate (or cyclic-phosphate) and 5'-hydroxy ends that cannot be sealed by classical DNA ligases (PubMed:24218597).7 Publications
Miscellaneous
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, PubMed:26858100). Acts as a DNA ligase by attaching a GMP nucleotide to a DNA 3'-P to form a 'capped' 3' end structure, DNA3'pp5'G. When a suitable DNA 5'-OH end is available, RtcB catalyzes attack of the 5'-OH on DNA3'pp5'G to form a 3'-5' phosphodiester splice junction (PubMed:24218597).3 Publications
Catalytic activityi
- (Ribonucleotide)(n)-3'-phosphate + 5'-hydroxy-(ribonucleotide)(m) + GTP = (ribonucleotide)(n+m) + GMP + diphosphate.4 Publications EC:6.5.1.8
- (Ribonucleotide)(n)-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)(m) + GTP + H(2)O = (ribonucleotide)(n+m) + GMP + diphosphate (overall reaction).4 Publications EC:6.5.1.8
Cofactori
Mn2+2 PublicationsNote: Binds 2 manganese ions per subunit.By similarity
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 75 | Manganese 1By similarity | 1 | |
Metal bindingi | 78 | Manganese 1By similarity | 1 | |
Metal bindingi | 78 | Manganese 2By similarity | 1 | |
Metal bindingi | 168 | Manganese 1; via tele nitrogenBy similarity | 1 | |
Metal bindingi | 185 | Manganese 2; via tele nitrogenBy similarity | 1 | |
Metal bindingi | 281 | Manganese 2; via tele nitrogenBy similarity | 1 | |
Binding sitei | 320 | GMPBy similarity | 1 | |
Active sitei | 337 | GMP-histidine intermediate1 Publication | 1 | |
Binding sitei | 407 | GMPBy similarity | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 167 – 171 | GMPBy similarity | 5 | |
Nucleotide bindingi | 281 – 282 | GMPBy similarity | 2 | |
Nucleotide bindingi | 313 – 316 | GMPBy similarity | 4 | |
Nucleotide bindingi | 337 – 340 | GMPBy similarity | 4 |
GO - Molecular functioni
- DNA ligase activity Source: EcoCyc
- GTP binding Source: UniProtKB-KW
- 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
- tRNA processing Source: UniProtKB-KW
Keywordsi
Molecular function | Ligase |
Biological process | tRNA processing |
Ligand | GTP-binding, Manganese, Metal-binding, Nucleotide-binding |
Enzyme and pathway databases
BioCyci | EcoCyc:G7751-MONOMER MetaCyc:G7751-MONOMER |
BRENDAi | 6.5.1.4, 2026 |
Names & Taxonomyi
Protein namesi | Recommended name: RNA-splicing ligase RtcBCurated (EC:6.5.1.83 Publications)Alternative name(s): 3'-phosphate/5'-hydroxy nucleic acid ligaseCurated |
Gene namesi | Name:rtcB1 Publication Synonyms:yhgL Ordered Locus Names:b3421, JW3384 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 75 | D → A: Almost no guanylation activity. Can ligate pre-guanylated nucleotide substrates. 1 Publication | 1 | |
Mutagenesisi | 78 | C → A: No activity. 1 Publication | 1 | |
Mutagenesisi | 167 | N → A: Retains approximately half of overall wild-type activity. Shows increased nucleotide guanylation activity. 1 Publication | 1 | |
Mutagenesisi | 168 | H → A: Retains approximately half of overall wild-type activity. 1 Publication | 1 | |
Mutagenesisi | 185 | H → A: Almost wild type activity. Is impaired in DNA 3'-phosphate capping. 1 Publication | 1 | |
Mutagenesisi | 189 | R → A: Almost wild type activity. Shows increased nucleotide guanylation activity. 1 Publication | 1 | |
Mutagenesisi | 281 | H → A: Less than 10% of overall wild-type activity. Can ligate pre-guanylated nucleotide substrates. 1 Publication | 1 | |
Mutagenesisi | 299 | K → A: Retains approximately half of overall wild-type activity. 1 Publication | 1 | |
Mutagenesisi | 337 | H → A: No overall activity. Abolishes formation of guanylylated RtcB intermediate. Can ligate pre-guanylated nucleotide substrates. 2 Publications | 1 | |
Mutagenesisi | 337 | H → N or Q: Loss of function. Abolishes formation of guanylylated RtcB intermediate. 1 Publication | 1 | |
Mutagenesisi | 341 | R → A: Less than 10% of overall wild-type activity. Shows increased nucleotide guanylation activity. 1 Publication | 1 | |
Mutagenesisi | 345 | R → A: Almost wild type activity. Is impaired in DNA 3'-phosphate capping. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000215109 | 1 – 408 | RNA-splicing ligase RtcBAdd BLAST | 408 |
Proteomic databases
PaxDbi | P46850 |
PRIDEi | P46850 |
2D gel databases
SWISS-2DPAGEi | P46850 |
Expressioni
Inductioni
Expression is repressed by RtcR.2 Publications
Interactioni
Subunit structurei
Monomer.
1 PublicationProtein-protein interaction databases
BioGRIDi | 4261188, 7 interactors |
IntActi | P46850, 20 interactors |
STRINGi | 511145.b3421 |
Family & Domainsi
Sequence similaritiesi
Belongs to the RtcB family.Curated
Phylogenomic databases
eggNOGi | COG1690, Bacteria |
HOGENOMi | CLU_022279_1_1_6 |
InParanoidi | P46850 |
PhylomeDBi | P46850 |
Family and domain databases
Gene3Di | 3.90.1860.10, 1 hit |
InterProi | View protein in InterPro IPR001233, RtcB IPR036025, RtcB-like_sf |
Pfami | View protein in Pfam PF01139, RtcB, 1 hit |
SUPFAMi | SSF103365, SSF103365, 1 hit |
PROSITEi | View protein in PROSITE PS01288, UPF0027, 1 hit |
i Sequence
Sequence statusi: Complete.
P46850-1 [UniParc]FASTAAdd to basket
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 84 | R → G in AAA58219 (PubMed:9278503).Curated | 1 |
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 |
PIRi | H65137 |
RefSeqi | NP_417879.1, NC_000913.3 WP_001105504.1, NZ_SSZK01000008.1 |
Genome annotation databases
EnsemblBacteriai | AAC76446; AAC76446; b3421 BAE77871; BAE77871; BAE77871 |
GeneIDi | 947929 |
KEGGi | ecj:JW3384 eco:b3421 |
PATRICi | fig|511145.12.peg.3516 |
Similar proteinsi
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 |
PIRi | H65137 |
RefSeqi | NP_417879.1, NC_000913.3 WP_001105504.1, NZ_SSZK01000008.1 |
3D structure databases
SMRi | P46850 |
ModBasei | Search... |
Protein-protein interaction databases
BioGRIDi | 4261188, 7 interactors |
IntActi | P46850, 20 interactors |
STRINGi | 511145.b3421 |
2D gel databases
SWISS-2DPAGEi | P46850 |
Proteomic databases
PaxDbi | P46850 |
PRIDEi | P46850 |
Genome annotation databases
EnsemblBacteriai | AAC76446; AAC76446; b3421 BAE77871; BAE77871; BAE77871 |
GeneIDi | 947929 |
KEGGi | ecj:JW3384 eco:b3421 |
PATRICi | fig|511145.12.peg.3516 |
Organism-specific databases
EchoBASEi | EB2774 |
Phylogenomic databases
eggNOGi | COG1690, Bacteria |
HOGENOMi | CLU_022279_1_1_6 |
InParanoidi | P46850 |
PhylomeDBi | P46850 |
Enzyme and pathway databases
BioCyci | EcoCyc:G7751-MONOMER MetaCyc:G7751-MONOMER |
BRENDAi | 6.5.1.4, 2026 |
Miscellaneous databases
PROi | PR:P46850 |
Family and domain databases
Gene3Di | 3.90.1860.10, 1 hit |
InterProi | View protein in InterPro IPR001233, RtcB IPR036025, RtcB-like_sf |
Pfami | View protein in Pfam PF01139, RtcB, 1 hit |
SUPFAMi | SSF103365, SSF103365, 1 hit |
PROSITEi | View protein in PROSITE PS01288, UPF0027, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | RTCB_ECOLI | |
Accessioni | P46850Primary (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: | December 2, 2020 | |
This is version 121 of the entry and version 3 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families