O59245 · RTCB_PYRHO
- ProteintRNA-splicing ligase RtcB
- GenertcB
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids871 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Essential for tRNA splicing and maturation (Probable). Acts by directly joining spliced tRNA halves to mature-sized tRNAs (PubMed:22320833, PubMed:22949672).
Joins RNA with 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy ends (PubMed:22320833, PubMed:22949672).
Joins RNA with 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy ends (PubMed:22320833, PubMed:22949672).
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.
Catalytic activity
- a 3'-end 3'-phospho-ribonucleotide-RNA + a 5'-end dephospho-ribonucleoside-RNA + GTP = a ribonucleotidyl-ribonucleotide-RNA + diphosphate + GMP
Cofactor
Note: Binds 2 manganese ions per subunit.
Activity regulation
Activated by archease, which accelerates both the RNA 3'-P guanylylation and ligation steps (PubMed:24435797).
Archease also expands the NTP specificity of RtcB, enabling the efficient use of dGTP, ATP or ITP (PubMed:24435797).
Archease also expands the NTP specificity of RtcB, enabling the efficient use of dGTP, ATP or ITP (PubMed:24435797).
Features
Showing features for binding site, active site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 95 | Mn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 488 | Mn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 488 | Mn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 592-596 | GMP (UniProtKB | ChEBI) | ||||
Sequence: NHFLE | ||||||
Binding site | 593 | Mn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 624 | Mn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 719 | Mn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 719-720 | GMP (UniProtKB | ChEBI) | ||||
Sequence: HN | ||||||
Binding site | 768-771 | GMP (UniProtKB | ChEBI) | ||||
Sequence: PGSM | ||||||
Binding site | 775 | GMP (UniProtKB | ChEBI) | ||||
Sequence: S | ||||||
Active site | 794 | GMP-histidine intermediate | ||||
Sequence: H | ||||||
Binding site | 794-797 | GMP (UniProtKB | ChEBI) | ||||
Sequence: HGAG | ||||||
Binding site | 870 | GMP (UniProtKB | ChEBI) | ||||
Sequence: K |
GO annotations
Aspect | Term | |
---|---|---|
Molecular Function | DNA binding | |
Molecular Function | endonuclease activity | |
Molecular Function | GMP binding | |
Molecular Function | GTP binding | |
Molecular Function | manganese ion binding | |
Molecular Function | RNA ligase (ATP) activity | |
Molecular Function | RNA ligase (GTP) activity | |
Biological Process | intein-mediated protein splicing | |
Biological Process | intron homing | |
Biological Process | RNA splicing, via endonucleolytic cleavage and ligation | |
Biological Process | tRNA processing |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nametRNA-splicing ligase RtcB
- EC number
- Alternative names
- Cleaved into 1 chains
Gene names
Organism names
- Strain
- Taxonomic lineageArchaea > Euryarchaeota > Thermococci > Thermococcales > Thermococcaceae > Pyrococcus
Accessions
- Primary accessionO59245
Proteomes
Phenotypes & Variants
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 65 | Abolishes formation of guanylylated RtcB intermediate. | ||||
Sequence: D → A | ||||||
Mutagenesis | 95 | Abolishes tRNA ligation activity. | ||||
Sequence: D → A | ||||||
Mutagenesis | 592 | Abolishes tRNA ligation activity in vitro. | ||||
Sequence: N → A | ||||||
Mutagenesis | 593 | Abolishes tRNA ligation activity. | ||||
Sequence: H → A | ||||||
Mutagenesis | 594 | Abolishes tRNA ligation activity in vitro. Can be rescued in presence of archease (PH1536). | ||||
Sequence: F → A | ||||||
Mutagenesis | 596 | Abolishes tRNA ligation activity in vitro. Can be rescued in presence of archease (PH1536). | ||||
Sequence: E → A | ||||||
Mutagenesis | 719 | Only produces few amount of guanylylated RtcB intermediate. | ||||
Sequence: H → A | ||||||
Mutagenesis | 794 | Loss of function. Abolishes formation of guanylylated RtcB intermediate. | ||||
Sequence: H → A | ||||||
Mutagenesis | 794 | Loss of function. Still able to form some guanylylated RtcB intermediate but is unable to carry out subsequent transfer of GMP. | ||||
Sequence: H → K | ||||||
Mutagenesis | 798 | Impaired formation of guanylylated RtcB intermediate. | ||||
Sequence: R → A | ||||||
Mutagenesis | 802 | Impaired formation of guanylylated RtcB intermediate. | ||||
Sequence: R → A | ||||||
Mutagenesis | 870 | Abolishes tRNA ligation activity in vitro. Can be rescued in presence of archease (PH1536). | ||||
Sequence: K → A |
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000232535 | 1-97 | tRNA-splicing ligase RtcB, 1st part | |||
Sequence: MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVAMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDIN | ||||||
Chain | PRO_0000232536 | 98-487 | Pho hyp2 intein | |||
Sequence: CLAPGTRVLTEHGYWLKIEEMPEKFKLQRLRVYNIEEGHNDFSKVVFVAEREVGSEEKAIRIVTESGKVIEGSEDHPVLTPEGYVYLRNVKEGDYILVYPFEGVPYEEKKGVILDESAFEGEDPQVVKFLRERNLIPLQWKDPKVGILARILGFALANGYISENDNLTFHGKEEVLREVRKDLEELGIEAIVAEEDKLKVTSREFAFLLEKLGMAHDSIPEWIIEGPLWIKRNFLAGLFGANGSIVEFKGDVPLPITLTHSRELLNDVSRILEGFKVRAKIKMGKNGSYQLVIEDEDSIRNFLGRINYEYDPEKKARGLIAYAYLKFKELMKGNLMTFEEFARDRGYEGGFVAEKVIEVKSVKPEYDKFYDIGVYHSAHNFIANGIVVHN | ||||||
Chain | PRO_0000232537 | 488-871 | tRNA-splicing ligase RtcB, 2nd part | |||
Sequence: CGVRLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDGAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVDNVVKVVSEAGIAKLVARMRPIGVAKG |
Post-translational modification
This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.
Keywords
- PTM
Interaction
Structure
Family & Domains
Features
Showing features for domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 248-374 | DOD-type homing endonuclease | ||||
Sequence: ILGFALANGYISENDNLTFHGKEEVLREVRKDLEELGIEAIVAEEDKLKVTSREFAFLLEKLGMAHDSIPEWIIEGPLWIKRNFLAGLFGANGSIVEFKGDVPLPITLTHSRELLNDVSRILEGFKV |
Sequence similarities
Belongs to the RtcB family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length871
- Mass (Da)98,125
- Last updated1998-08-01 v1
- Checksum989723B0089288F4
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
BA000001 EMBL· GenBank· DDBJ | BAA30714.1 EMBL· GenBank· DDBJ | Genomic DNA |