RTCB_METKA
ID RTCB_METKA Reviewed; 988 AA.
AC Q8TUS2;
DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 105.
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=Mka hyp2 intein;
DE EC=3.1.-.-;
GN Name=rtcB; OrderedLocusNames=MK1682;
OS Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938).
OC Archaea; Euryarchaeota; Methanopyri; Methanopyrales; Methanopyraceae;
OC Methanopyrus.
OX NCBI_TaxID=190192;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AV19 / DSM 6324 / JCM 9639 / NBRC 100938;
RX PubMed=11930014; DOI=10.1073/pnas.032671499;
RA Slesarev A.I., Mezhevaya K.V., Makarova K.S., Polushin N.N.,
RA Shcherbinina O.V., Shakhova V.V., Belova G.I., Aravind L., Natale D.A.,
RA Rogozin I.B., Tatusov R.L., Wolf Y.I., Stetter K.O., Malykh A.G.,
RA Koonin E.V., Kozyavkin S.A.;
RT "The complete genome of hyperthermophile Methanopyrus kandleri AV19 and
RT monophyly of archaeal methanogens.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:4644-4649(2002).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
RC STRAIN=AV19 / DSM 6324 / JCM 9639 / NBRC 100938;
RX PubMed=21209330; DOI=10.1073/pnas.1018307108;
RA Englert M., Sheppard K., Aslanian A., Yates J.R. III, Soll D.;
RT "Archaeal 3'-phosphate RNA splicing ligase characterization identifies the
RT missing component in tRNA maturation.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:1290-1295(2011).
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:0000269|PubMed:21209330}.
CC -!- PTM: This protein undergoes a protein self splicing that involves a
CC post-translational excision of the intervening region (intein) followed
CC by peptide ligation. {ECO:0000305}.
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; AE009439; AAM02895.1; -; Genomic_DNA.
DR AlphaFoldDB; Q8TUS2; -.
DR SMR; Q8TUS2; -.
DR STRING; 190192.MK1682; -.
DR EnsemblBacteria; AAM02895; AAM02895; MK1682.
DR KEGG; mka:MK1682; -.
DR PATRIC; fig|190192.8.peg.1847; -.
DR HOGENOM; CLU_012374_0_0_2; -.
DR OMA; VHNCGVR; -.
DR BRENDA; 6.5.1.8; 3274.
DR Proteomes; UP000001826; 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; TAS:UniProtKB.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; TAS:UniProtKB.
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.
DR PROSITE; PS01288; UPF0027; 1.
PE 1: Evidence at protein level;
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..100
FT /note="tRNA-splicing ligase RtcB, 1st part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000232526"
FT CHAIN 101..582
FT /note="Mka hyp2 intein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000232527"
FT CHAIN 583..988
FT /note="tRNA-splicing ligase RtcB, 2nd part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000232528"
FT DOMAIN 251..415
FT /note="DOD-type homing endonuclease"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273"
FT ACT_SITE 911
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 98
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 583
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 583
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 699..703
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 700
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 732
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 833..834
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 833
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 885..888
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 892
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 911..914
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 987
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
SQ SEQUENCE 988 AA; 110989 MW; C24DAC047EAC3132 CRC64;
MAPKSMLKHI RNNVVWELPE DYKGCMKVPG RIYATEKLID GMEKGVFDQV ANVACLPGIY
GYSIALPDAH YGYGFPIGGV AAFDVEEGVV SPGGVGYDIN CLAPGTKILT EHGCWVKVED
LPKMLTDQKL KVYDVDEGRE DDSEIKFVME RGIEEDERAV VLVTESGLTI EGSEDHPVLT
PEGYVELGEI EEGDLVVVYP FEGVEYEEKE GTILDESDFE DVDPQVLRYL EERDLIPLRW
SDPKVGTLAR ILGFAMGDGH LGEQAGRLTL SFYGDERTLR ELKRDLESLG VKANLHVRKR
RYEIETASGR YEGEATSVEL RVASRSFALL MEKLGMPRGR KVETPYKVPD WIKEAPLWVK
RNFLAGLFAA DGSVVKFKRY TPLPINLTQA KVEELEENLR EFMNDVAKLL REFGIETTLY
EVKSKKNVVY KLAIVGEENI KRFLGKVGYE YDPEKKVEGL AAYAYLKLKE RVKKDRKEAA
ETAAEVYEET GSITKAHEAV ADVVNRRFVE RVVYDGGISS VRVPEDFPTF ERFKEERVLA
GGFVIEEVVE VKGVEPEYDR FYDIGVCHGA HNFIADGVVV HNCGVRVMKT DLTEDDVRPK
LRELLETIFR NVPAGLGSRH RRVRLSTQEL RQVMLYGAEW AVEEGFGFDE DLDHIESRGN
MTHAYETIGW EEYGPRDDVA SKRAIERGRP QLGTLGSGNH FLEVQVVDEI YDKEAAEKMG
IREEGQVTIM VHTGSRGFGH QVCSDHLRIM ERSMRDVERR FGVRIPDRQL ACAAMGTDEA
KRYFNAMNAA ANYAFANRQM ISHWTRESFV EVFGDEYGDA DDMGIEVIYD IAHNMAKIEK
HPVDGEERWL VVHRKGATRA FSEEALKKHG EPVPFEGLPQ PVLIPGDMGT GSYILIGTEK
AMEETWGSTC HGAGRTMSRA AAKRKFWGED VARELERQGI LVKAASMPVV AEEAPPAYKD
VDEVVRAVAE AGISDPVVRL RPIGVVKG
