RTCB_PYRAB
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 03-AUG-2022, entry version 112.
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}.
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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 EnsemblBacteria; CAB49482; CAB49482; 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 OMA; VHNCGVR; -.
DR OrthoDB; 22545at2157; -.
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 Gene3D; 3.10.28.10; -; 1.
DR Gene3D; 3.90.1860.10; -; 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 PANTHER; PTHR11118; PTHR11118; 1.
DR Pfam; PF14528; LAGLIDADG_3; 1.
DR Pfam; PF01139; RtcB; 1.
DR PRINTS; PR00379; INTEIN.
DR SMART; SM00305; HintC; 1.
DR SMART; SM00306; HintN; 1.
DR SUPFAM; SSF103365; SSF103365; 2.
DR SUPFAM; SSF51294; SSF51294; 1.
DR SUPFAM; SSF55608; SSF55608; 1.
DR TIGRFAMs; TIGR01443; intein_Cterm; 1.
DR TIGRFAMs; TIGR01445; intein_Nterm; 1.
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
