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}.
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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
//
