RTCB_ARCFU
ID RTCB_ARCFU Reviewed; 482 AA.
AC O29399;
DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 92.
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};
GN Name=rtcB; OrderedLocusNames=AF_0862;
OS Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC
OS 100126 / VC-16).
OC Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC Archaeoglobus.
OX NCBI_TaxID=224325;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16;
RX PubMed=9389475; DOI=10.1038/37052;
RA Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A.,
RA Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L.,
RA Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D.,
RA Quackenbush J., Lee N.H., Sutton G.G., Gill S.R., Kirkness E.F.,
RA Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N.,
RA Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R.,
RA Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D.,
RA Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P.,
RA Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M.,
RA Smith H.O., Woese C.R., Venter J.C.;
RT "The complete genome sequence of the hyperthermophilic, sulphate-reducing
RT archaeon Archaeoglobus fulgidus.";
RL Nature 390:364-370(1997).
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; AE000782; AAB90372.1; -; Genomic_DNA.
DR PIR; F69357; F69357.
DR AlphaFoldDB; O29399; -.
DR SMR; O29399; -.
DR STRING; 224325.AF_0862; -.
DR PRIDE; O29399; -.
DR EnsemblBacteria; AAB90372; AAB90372; AF_0862.
DR KEGG; afu:AF_0862; -.
DR eggNOG; arCOG04246; Archaea.
DR HOGENOM; CLU_022279_0_1_2; -.
DR OMA; QTRGVEC; -.
DR PhylomeDB; O29399; -.
DR Proteomes; UP000002199; Chromosome.
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:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 3.90.1860.10; -; 1.
DR InterPro; IPR001233; RtcB.
DR InterPro; IPR036025; RtcB-like_sf.
DR PANTHER; PTHR11118; PTHR11118; 1.
DR Pfam; PF01139; RtcB; 1.
DR SUPFAM; SSF103365; SSF103365; 1.
PE 3: Inferred from homology;
KW GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome; tRNA processing.
FT CHAIN 1..482
FT /note="tRNA-splicing ligase RtcB"
FT /id="PRO_0000232539"
FT ACT_SITE 405
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 97
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 100
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 100
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 204..208
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 205
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 236
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 330..331
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 330
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 379..382
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 386
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 405..408
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 481
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
SQ SEQUENCE 482 AA; 53025 MW; A6A62AC2B0453E4C CRC64;
MNMEGILKKI TDYKWELPKS YKPGMRVPAY FYISRKLMQI LEKDAVEQAA NVATMPGIQV
ASLVMPDVHV GYGFPIGGVA GFDVNEGVVS PGGVGFDINC GVRLLRSNLN VEDVKPLIKK
LIDELFVAVP SGVGSEGRLR VSDRELDEIF VEGARWAVEN GYGYERDLKH CEEEGALEGA
RPEVVSKKAR DRGRPQLGTL GSGNHFLEVQ YVDKVFDEKV AAKFGIEEGM VTVMIHCGSR
GLGHQVCTDF LEVLDRAVKK YGIKLPDRQL ACAPINSKEG QDYFAGMAAS ANYAWCNRQI
IAHWVRETFQ KVMGMSEDDL GMELVYDVAH NIAKFEEHRV DGKKMKLCVH RKGATRAFGP
GLKEVPEDYR DVGQPVLIPG SMGTPSYILV GTEKAMEETF GSTCHGSGRV MSRAAAKRKL
RGNVVKQNLE RKGIYVRATH GALLAEEAPE AYKLSDDVVD VVHRAGISKL VARLRPLGVA
KG
