RTCB_METJA
ID RTCB_METJA Reviewed; 968 AA.
AC Q58095;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 123.
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=Mja hyp2 intein;
DE EC=3.1.-.-;
GN Name=rtcB; OrderedLocusNames=MJ0682;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
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; L77117; AAB98677.1; -; Genomic_DNA.
DR PIR; B64385; B64385.
DR RefSeq; WP_010870187.1; NC_000909.1.
DR AlphaFoldDB; Q58095; -.
DR SMR; Q58095; -.
DR STRING; 243232.MJ_0682; -.
DR EnsemblBacteria; AAB98677; AAB98677; MJ_0682.
DR GeneID; 1451548; -.
DR KEGG; mja:MJ_0682; -.
DR eggNOG; arCOG03158; Archaea.
DR eggNOG; arCOG04246; Archaea.
DR HOGENOM; CLU_012374_0_0_2; -.
DR InParanoid; Q58095; -.
DR OMA; VHNCGVR; -.
DR OrthoDB; 22545at2157; -.
DR PhylomeDB; Q58095; -.
DR Proteomes; UP000000805; 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:0003972; F:RNA ligase (ATP) activity; IBA:GO_Central.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR GO; GO:0000971; P:tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate; IBA:GO_Central.
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 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..97
FT /note="tRNA-splicing ligase RtcB, 1st part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000036183"
FT CHAIN 98..585
FT /note="Mja hyp2 intein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000036184"
FT CHAIN 586..968
FT /note="tRNA-splicing ligase RtcB, 2nd part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000036185"
FT DOMAIN 245..414
FT /note="DOD-type homing endonuclease"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273"
FT ACT_SITE 891
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 586
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 586
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 690..694
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 691
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 722
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 816..817
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 816
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 865..868
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 872
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 891..894
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 967
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
SQ SEQUENCE 968 AA; 110206 MW; 39A2A66280466130 CRC64;
MKDVLKRVSD VVWELPKDYK DCMRVPGRIY LNEILLDELE PEVLEQIANV ACLPGIYKYS
IAMPDVHYGY GFAIGGVAAF DQREGVISPG GVGFDINCLT SNSKILTDDG YYIKLEKLKE
KLDLHIKIYN TEEGEKSSNI LFVSERYADE KIIRIKTESG RVLEGSKDHP VLTLNGYVPM
GMLKEGDDVI VYPYEGVEYE EPSDEIILDE DDFAEYDKQI IKYLKDRGLL PLRMDNKNIG
IIARLLGFAF GDGSIVKENG DRERLYVAFY GKRETLIKIR EDLEKLGIKA SRIYSRKREV
EIRNAYGDEY TSLCEDNSIK ITSKAFALFM HKLGMPIGKK TEQIYKIPEW IKKAPKWVKR
NFLAGLFGAD GSRAVFKNYT PLPINLTMSK SEELKENILE FLNEIKLLLA EFDIESMIYE
IKSLDGRVSY RLAIVGEESI KNFLGRINYE YSGEKKVIGL LAYEYLRRKD IAKEIRKKCI
KRAKELYKKG VTVSEMLKMD EFRNEFISKR LIERAVYENL DEDDVRISTK FPKFEEFIEK
YGVIGGFVID KIKEIEEISY DSKLYDVGIV SKEHNFIANS IVVHNCGVRL IRTNLTKEEV
QSKIKELIKT LFKNVPSGLG SKGILKFSKS VMDDVLEEGV RWAVKEGYGW KEDLEFIEEH
GCLKDADASY VSDKAKERGR VQLGSLGSGN HFLEVQYVEK VFDEEAAEIY GIEENQVVVL
VHTGSRGLGH QICTDYLRIM EKAAKNYGIK LPDRQLACAP FESEEGQSYF KAMCCGANYA
WANRQMITHW VRESFEEVFK IHAEDLEMNI VYDVAHNIAK KEEHIIDGRK VKVIVHRKGA
TRAFPPKHEA IPKEYWSVGQ PVIIPGDMGT ASYLMRGTEI AMKETFGSTA HGAGRKLSRA
KALKLWKGKE IQRRLAEMGI VAMSDSKAVM AEEAPEAYKS VDLVADTCHK AGISLKVARM
RPLGVIKG
