ID RTCB_PYRFU Reviewed; 970 AA. AC Q8U0H4; DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot. DT 01-JUN-2002, sequence version 1. DT 27-MAR-2024, entry version 108. DE RecName: Full=tRNA-splicing ligase RtcB {ECO:0000250|UniProtKB:O59245}; DE EC=6.5.1.8 {ECO:0000250|UniProtKB:O59245}; DE AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000250|UniProtKB:O59245}; DE Contains: DE RecName: Full=Pfu hyp2 intein; DE EC=3.1.-.-; GN Name=rtcB; OrderedLocusNames=PF1615; OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1). OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; OC Pyrococcus. OX NCBI_TaxID=186497; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1; RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299; RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., RA DiRuggiero J., Robb F.T.; RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. RT horikoshii inferred from complete genomic sequences."; RL Genetics 152:1299-1305(1999). CC -!- FUNCTION: Essential for tRNA splicing and maturation. Acts by directly CC joining spliced tRNA halves to mature-sized tRNAs. Joins RNA with CC 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy CC ends. {ECO:0000250|UniProtKB:O59245}. CC -!- CATALYTIC ACTIVITY: CC Reaction=a 3'-end 3'-phospho-ribonucleotide-RNA + a 5'-end dephospho- CC ribonucleoside-RNA + GTP = a ribonucleotidyl-ribonucleotide-RNA + CC diphosphate + GMP; Xref=Rhea:RHEA:68076, Rhea:RHEA-COMP:10463, CC Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:17355, ChEBI:CHEBI:33019, CC ChEBI:CHEBI:37565, ChEBI:CHEBI:58115, ChEBI:CHEBI:83062, CC ChEBI:CHEBI:138284, ChEBI:CHEBI:173118; EC=6.5.1.8; CC Evidence={ECO:0000250|UniProtKB:O59245}; CC -!- CATALYTIC ACTIVITY: CC Reaction=a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + a 5'-end CC dephospho-ribonucleoside-RNA + GTP + H2O = a ribonucleotidyl- CC ribonucleotide-RNA + diphosphate + GMP + H(+); Xref=Rhea:RHEA:68080, CC Rhea:RHEA-COMP:10464, Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:17355, CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019, CC ChEBI:CHEBI:37565, ChEBI:CHEBI:58115, ChEBI:CHEBI:83064, CC ChEBI:CHEBI:138284, ChEBI:CHEBI:173118; EC=6.5.1.8; CC Evidence={ECO:0000250|UniProtKB:O59245}; CC -!- COFACTOR: CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; CC Evidence={ECO:0000250|UniProtKB:O59245}; CC Note=Binds 2 manganese ions per subunit. CC {ECO:0000250|UniProtKB:O59245}; CC -!- SUBUNIT: Monomer. {ECO:0000250|UniProtKB:O59245}. CC -!- MISCELLANEOUS: Ligation proceeds through 3 nucleotidyl transfer steps, CC with 2',3'-cyclic phosphate termini being hydrolyzed to 3'-P termini in CC a step that precedes 3'-P activation with GMP. In the first nucleotidyl CC transfer step, RtcB reacts with GTP to form a covalent RtcB-histidine- CC GMP intermediate with release of PPi; in the second step, the GMP CC moiety is transferred to the RNA 3'-P; in the third step, the 5'-OH CC from the opposite RNA strand attacks the activated 3'-P to form a CC 3',5'-phosphodiester bond and release GMP. CC {ECO:0000250|UniProtKB:O59245}. CC -!- SIMILARITY: Belongs to the RtcB family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AE009950; AAL81739.1; -; Genomic_DNA. DR AlphaFoldDB; Q8U0H4; -. DR SMR; Q8U0H4; -. DR IntAct; Q8U0H4; 1. DR STRING; 186497.PF1615; -. DR PaxDb; 186497-PF1615; -. DR KEGG; pfu:PF1615; -. DR PATRIC; fig|186497.12.peg.1682; -. DR eggNOG; arCOG03158; Archaea. DR eggNOG; arCOG04246; Archaea. DR HOGENOM; CLU_012374_0_0_2; -. DR PhylomeDB; Q8U0H4; -. DR BRENDA; 6.5.1.8; 5243. DR Proteomes; UP000001013; Chromosome. DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW. DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW. DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0008452; F:RNA ligase activity; IEA:InterPro. DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro. DR GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW. DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW. DR CDD; cd00081; Hint; 2. DR Gene3D; 3.10.28.10; Homing endonucleases; 1. DR Gene3D; 3.90.1860.10; tRNA-splicing ligase RtcB; 2. DR InterPro; IPR003586; Hint_dom_C. DR InterPro; IPR003587; Hint_dom_N. DR InterPro; IPR036844; Hint_dom_sf. DR InterPro; IPR027434; Homing_endonucl. DR InterPro; IPR006142; INTEIN. DR InterPro; IPR030934; Intein_C. DR InterPro; IPR004042; Intein_endonuc. DR InterPro; IPR006141; Intein_N. DR InterPro; IPR004860; LAGLIDADG_2. DR InterPro; IPR001233; RtcB. DR InterPro; IPR036025; RtcB-like_sf. DR NCBIfam; TIGR01443; intein_Cterm; 1. DR NCBIfam; TIGR01445; intein_Nterm; 1. DR NCBIfam; NF038162; RctB_rel_intein; 1. DR PANTHER; PTHR11118:SF1; RNA-SPLICING LIGASE RTCB HOMOLOG; 1. DR PANTHER; PTHR11118; UNCHARACTERIZED; 1. DR Pfam; PF14890; Intein_splicing; 1. DR Pfam; PF14528; LAGLIDADG_3; 1. DR Pfam; PF01139; RtcB; 2. DR PRINTS; PR00379; INTEIN. DR SMART; SM00305; HintC; 1. DR SMART; SM00306; HintN; 1. DR SUPFAM; SSF51294; Hedgehog/intein (Hint) domain; 1. DR SUPFAM; SSF55608; Homing endonucleases; 1. DR SUPFAM; SSF103365; Hypothetical protein PH1602; 2. DR PROSITE; PS50818; INTEIN_C_TER; 1. DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1. DR PROSITE; PS50817; INTEIN_N_TER; 1. PE 3: Inferred from homology; KW Autocatalytic cleavage; DNA-binding; Endonuclease; GTP-binding; Hydrolase; KW Intron homing; Ligase; Manganese; Metal-binding; Nuclease; KW Nucleotide-binding; Protein splicing; Reference proteome; tRNA processing. FT CHAIN 1..105 FT /note="tRNA-splicing ligase RtcB, 1st part" FT /evidence="ECO:0000255" FT /id="PRO_0000232532" FT CHAIN 106..586 FT /note="Pfu hyp2 intein" FT /evidence="ECO:0000255" FT /id="PRO_0000232533" FT CHAIN 587..970 FT /note="tRNA-splicing ligase RtcB, 2nd part" FT /evidence="ECO:0000255" FT /id="PRO_0000232534" FT DOMAIN 256..420 FT /note="DOD-type homing endonuclease" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273" FT ACT_SITE 893 FT /note="GMP-histidine intermediate" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 103 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 587 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 587 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 691..695 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 692 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 723 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 818..819 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 818 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 867..870 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 874 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 893..896 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 969 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" SQ SEQUENCE 970 AA; 109712 MW; CC0AEE4573CFE7C2 CRC64; MIILRVVNVA VPLKRIDKIR WEIPKFDKRM KVPGRVYADD VLIEKMRQDR TLEQAANVAM LPGIYKYSIV MPDGHQGYGF PIGGVAAFDI KEGVISPGGI GYDINCLAPG TKVLTEHGYW LKIEEMPEKF KLQRLRLYNI EEGHNDFSRV AFVAERNIEK DETAIRIVTE TGTLIEGSED HPVLTPQGYV YLKNIKEGDY VIVYPFEGVP YEEKKGIIID ESAFEGEDPQ VIKFLKERNL LPLRWEDPKI GTLARILGFA LGDGHLGEMG GRLVLAFYGR EETLRELKKD LESLGIKANL YVREKNYRIK TESGEYSGKT VLAELRVSSR SFALLLEKLG MPRGEKTKKA YRIPVWIMEA PLWVKRNFLA GFFGADGSIV EFKGTTPLPI HLTQAKDVAL EENLKEFLYD ISRILEEFGV KTTIYKVNSK KSVTYRLSIV GEENIRNFLG KINYEYDPKK KAKGLIAYAY LKFKESVKKE RRKAMEISKK IYEETGNIDR AYKAVKDIVN RRFVERTIYE GERNPRVPKN FLTFEEFAKE RGYEGGFVAE KVVKVERIKP EYDRFYDIGV YHEAHNFIAN GIVVHNCGVR LIRTNLTEKD VRPKIKQLVD TLFKNVPSGV GSQGKVRLHW TQIDDVLVDG AKWAVDQGYG WERDLERLEE GGRMEGADPD AVSQRAKQRG APQLGSLGSG NHFLEVQVVD KIFDEEIAKA YGLFEGQVVV MVHTGSRGLG HQVASDYLRI MERAIRKYGI PWPDRELVSV PFQSEEGQRY FSAMKAAANF AWANRQMITH WVRESFQEVF RQDPEGDLGM EIVYDVAHNI GKVEEHEVDG KKVKVIVHRK GATRAFPPGH EAIPKIYRDV GQPVLIPGSM GTASYVLAGT EGAMAETFGS TCHGAGRVLS RAAATRQYRG DRIRDELLRR GIYVRAASMR VVAEEAPGAY KNVDNVVKVV SEAGIAKLVA RMRPIGVAKG //