ID RTCB_PYRAB Reviewed; 916 AA. AC Q9V168; G8ZJ23; DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot. DT 01-MAY-2000, sequence version 1. DT 27-MAR-2024, entry version 118. 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=Pab hyp2 intein; DE EC=3.1.-.-; GN Name=rtcB; OrderedLocusNames=PYRAB05600; ORFNames=PAB0383; OS Pyrococcus abyssi (strain GE5 / Orsay). OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; OC Pyrococcus. OX NCBI_TaxID=272844; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=GE5 / Orsay; RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x; RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O., RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J., RA Weissenbach J., Zivanovic Y., Forterre P.; RT "An integrated analysis of the genome of the hyperthermophilic archaeon RT Pyrococcus abyssi."; RL Mol. Microbiol. 47:1495-1512(2003). RN [2] RP GENOME REANNOTATION. RC STRAIN=GE5 / Orsay; RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x; RA Gao J., Wang J.; RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and RT Pyrococcus furiosus DSM 3638."; RL Curr. Microbiol. 64:118-129(2012). 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; AJ248284; CAB49482.1; -; Genomic_DNA. DR EMBL; HE613800; CCE69950.1; -; Genomic_DNA. DR PIR; C75175; C75175. DR RefSeq; WP_010867684.1; NC_000868.1. DR AlphaFoldDB; Q9V168; -. DR SMR; Q9V168; -. DR STRING; 272844.PAB0383; -. DR GeneID; 1495463; -. DR KEGG; pab:PAB0383; -. DR PATRIC; fig|272844.11.peg.596; -. DR eggNOG; arCOG03158; Archaea. DR eggNOG; arCOG04246; Archaea. DR HOGENOM; CLU_012374_0_0_2; -. DR OrthoDB; 9887at2157; -. DR PhylomeDB; Q9V168; -. DR Proteomes; UP000000810; Chromosome. DR Proteomes; UP000009139; 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 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; tRNA processing. FT CHAIN 1..97 FT /note="tRNA-splicing ligase RtcB, 1st part" FT /evidence="ECO:0000255" FT /id="PRO_0000232529" FT CHAIN 98..533 FT /note="Pab hyp2 intein" FT /evidence="ECO:0000255" FT /id="PRO_0000232530" FT CHAIN 534..916 FT /note="tRNA-splicing ligase RtcB, 2nd part" FT /evidence="ECO:0000255" FT /id="PRO_0000232531" FT DOMAIN 248..409 FT /note="DOD-type homing endonuclease" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273" FT ACT_SITE 839 FT /note="GMP-histidine intermediate" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 95 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 534 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 534 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 638..642 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 639 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 670 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 764..765 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 764 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 813..816 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 820 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 839..842 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" FT BINDING 915 FT /ligand="GMP" FT /ligand_id="ChEBI:CHEBI:58115" FT /evidence="ECO:0000250|UniProtKB:O59245" SQ SEQUENCE 916 AA; 102456 MW; 32DB1F28BE85155A CRC64; MTVPLKRIDK IRWEIPKFDK RMRVPGRVYA DDVLLEKMKS DRTLEQAANV AMLPGIYKYS IVMPDGHQGY GFPIGGVAAF DVNEGVISPG GIGYDINCLA PGSKVLTEHG YWLKVEELPE KFKLQGVKVY NLDEGHNDTS NVAFVAEREV ETGEMAVRVT TESGRIIEGS EDHPVLTPEG YVYLGNLKEG NLVIVYPFEG VEYEERKGVI LDEDAFKDED PQVLSFLREK GLVPLRWDDP RIGTIARILG FAFGDGYLGE MGGRLTLTFY GKEETLRELK KDLERLGISA NLYVRESIET TSGHSEGKSL SIELRVTSRS FALFLEKLGM PRGKKTEKAY RVPGWILEAP LWVKRNFLAG LFAADGSIVE FKGNTPLPIN LTQSKSDELA ENLVEFLGDV AKLLAEFGIE TTLYEVKSKK GVTYRLSIVG EDSIRTFVER INYEYDPEKK VKGLIAAAYL KLKERIVKEA HEAVKDDFPT FEEFAKERGY EGGFVAEKVV KVERVKPEYT KFYDIGVYHE AHNFIANGIV VHNCGVRLIR TNLTEKDVRP RIKQLVDTLF KNVPSGVGSQ GRVRLHWTQI DDVLVDGAKW AVDNGYGWEE DLERLEEGGR MEGADPDAVS QRAKQRGAPQ LGSLGSGNHF LEVQVVDKIF DPEVAKVYGL FEGQVVVMVH TGSRGLGHQV ASDYLRIMER AIRKYRIPWP DRELVSVPFQ SEEGQRYFSA MKAAANFAWA NRQMITHWVR ESFQEVFRQD PEDLGMSIVY DVAHNIGKVE EHEVDGKKVK VIVHRKGATR AFPPGHEAIP KIYRDVGQPV LIPGSMGTAS YVLAGTEGAM KETFGSTCHG AGRVLSRKAA TRQYRGDRIR QELLNRGIYV RAASMRVVAE EAPGAYKNVD NVVKVVSEAG IAKLVARMRP IGVAKG //