ID   RTCB_RAT                Reviewed;         505 AA.
AC   Q6AYT3; Q6PX76;
DT   31-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT   13-SEP-2004, sequence version 1.
DT   24-JAN-2024, entry version 115.
DE   RecName: Full=RNA-splicing ligase RtcB homolog {ECO:0000255|HAMAP-Rule:MF_03144};
DE            EC=6.5.1.8 {ECO:0000255|HAMAP-Rule:MF_03144};
DE   AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000255|HAMAP-Rule:MF_03144};
DE   AltName: Full=p55;
GN   Name=Rtcb {ECO:0000255|HAMAP-Rule:MF_03144};
OS   Rattus norvegicus (Rat).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC   Murinae; Rattus.
OX   NCBI_TaxID=10116;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RA   Ding N.-Z., He M., He C.-Q., Chen J.G.;
RT   "Cloning of the rat P55 gene.";
RL   Submitted (MAR-2004) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=Brown Norway; TISSUE=Kidney;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
CC   -!- FUNCTION: Catalytic subunit of the tRNA-splicing ligase complex that
CC       acts by directly joining spliced tRNA halves to mature-sized tRNAs by
CC       incorporating the precursor-derived splice junction phosphate into the
CC       mature tRNA as a canonical 3',5'-phosphodiester. May act as an RNA
CC       ligase with broad substrate specificity, and may function toward other
CC       RNAs. {ECO:0000255|HAMAP-Rule:MF_03144}.
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:0000255|HAMAP-Rule:MF_03144};
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:0000255|HAMAP-Rule:MF_03144};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_03144};
CC       Note=Binds 2 manganese ions per subunit. {ECO:0000255|HAMAP-
CC       Rule:MF_03144};
CC   -!- SUBUNIT: Catalytic component of the tRNA-splicing ligase complex.
CC       {ECO:0000255|HAMAP-Rule:MF_03144}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Cytoplasm
CC       {ECO:0000255|HAMAP-Rule:MF_03144}. Note=Enters into the nucleus in case
CC       of active transcription while it accumulates in cytosol when
CC       transcription level is low. {ECO:0000250}.
CC   -!- MISCELLANEOUS: Ligation probably proceeds through 3 nucleotidyl
CC       transfer steps, with 2',3'-cyclic phosphate termini being hydrolyzed to
CC       3'-P termini in a step that precedes 3'-P activation with GMP. In the
CC       first nucleotidyl transfer step, RTCB reacts with GTP to form a
CC       covalent RTCB-histidine-GMP intermediate with release of PPi; in the
CC       second step, the GMP moiety is transferred to the RNA 3'-P; in the
CC       third step, the 5'-OH from the opposite RNA strand attacks the
CC       activated 3'-P to form a 3',5'-phosphodiester bond and release GMP.
CC       {ECO:0000255|HAMAP-Rule:MF_03144}.
CC   -!- SIMILARITY: Belongs to the RtcB family. {ECO:0000255|HAMAP-
CC       Rule:MF_03144}.
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DR   EMBL; AY572415; AAS78621.1; -; mRNA.
DR   EMBL; BC078924; AAH78924.1; -; mRNA.
DR   RefSeq; NP_997497.1; NM_207614.1.
DR   AlphaFoldDB; Q6AYT3; -.
DR   SMR; Q6AYT3; -.
DR   BioGRID; 263779; 8.
DR   IntAct; Q6AYT3; 5.
DR   MINT; Q6AYT3; -.
DR   STRING; 10116.ENSRNOP00000006570; -.
DR   iPTMnet; Q6AYT3; -.
DR   PhosphoSitePlus; Q6AYT3; -.
DR   jPOST; Q6AYT3; -.
DR   PaxDb; 10116-ENSRNOP00000006570; -.
DR   Ensembl; ENSRNOT00055037834; ENSRNOP00055030876; ENSRNOG00055022012.
DR   Ensembl; ENSRNOT00060048696; ENSRNOP00060040609; ENSRNOG00060027957.
DR   Ensembl; ENSRNOT00065043022; ENSRNOP00065035222; ENSRNOG00065024982.
DR   GeneID; 362855; -.
DR   KEGG; rno:362855; -.
DR   UCSC; RGD:1303261; rat.
DR   AGR; RGD:1303261; -.
DR   CTD; 51493; -.
DR   RGD; 1303261; Rtcb.
DR   VEuPathDB; HostDB:ENSRNOG00000004813; -.
DR   eggNOG; KOG3833; Eukaryota.
DR   HOGENOM; CLU_022279_0_0_1; -.
DR   InParanoid; Q6AYT3; -.
DR   OrthoDB; 275654at2759; -.
DR   PhylomeDB; Q6AYT3; -.
DR   TreeFam; TF314404; -.
DR   PRO; PR:Q6AYT3; -.
DR   Proteomes; UP000002494; Chromosome 7.
DR   Bgee; ENSRNOG00000004813; Expressed in jejunum and 19 other cell types or tissues.
DR   GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR   GO; GO:0005789; C:endoplasmic reticulum membrane; ISO:RGD.
DR   GO; GO:0005635; C:nuclear envelope; ISO:RGD.
DR   GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR   GO; GO:0072669; C:tRNA-splicing ligase complex; ISS:UniProtKB.
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; ISS:UniProtKB.
DR   GO; GO:0017166; F:vinculin binding; ISO:RGD.
DR   GO; GO:0001701; P:in utero embryonic development; ISO:RGD.
DR   GO; GO:0001890; P:placenta development; ISO:RGD.
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   GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; ISS:UniProtKB.
DR   Gene3D; 3.90.1860.10; tRNA-splicing ligase RtcB; 1.
DR   HAMAP; MF_03144; RtcB_euk; 1.
DR   InterPro; IPR001233; RtcB.
DR   InterPro; IPR036025; RtcB-like_sf.
DR   InterPro; IPR027513; RtcB_euk.
DR   PANTHER; PTHR11118:SF1; RNA-SPLICING LIGASE RTCB HOMOLOG; 1.
DR   PANTHER; PTHR11118; UNCHARACTERIZED; 1.
DR   Pfam; PF01139; RtcB; 1.
DR   SUPFAM; SSF103365; Hypothetical protein PH1602; 1.
DR   PROSITE; PS01288; UPF0027; 1.
DR   Genevisible; Q6AYT3; RN.
PE   2: Evidence at transcript level;
KW   Cytoplasm; GTP-binding; Isopeptide bond; Ligase; Manganese; Metal-binding;
KW   Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
KW   tRNA processing; Ubl conjugation.
FT   CHAIN           1..505
FT                   /note="RNA-splicing ligase RtcB homolog"
FT                   /id="PRO_0000255245"
FT   ACT_SITE        428
FT                   /note="GMP-histidine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         119
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         122
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         122
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         226..230
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         227
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         259
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         353..354
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         353
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         402..405
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         409
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         428..431
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         504
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   MOD_RES         300
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y3I0"
FT   CROSSLNK        496
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Y3I0"
FT   CONFLICT        316
FT                   /note="Y -> C (in Ref. 1; AAS78621)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   505 AA;  55249 MW;  3488A9BF91460480 CRC64;
     MSRNYNDELQ FLDKINKNCW RIKKGFVPNM QVEGVFYVND ALEKLMFEEL RNACRGGGVG
     GFLPAMKQIG NVAALPGIVH RSIGLPDVHS GYGFAIGNMA AFDMNDPEAV VSPGGVGFDI
     NCGVRLLRTN LDESDVQPVK EQLAQAMFDH IPVGVGSKGV IPMNAKDLEE ALEMGVDWSL
     REGYAWAEDK EHCEEYGRML QADPNKVSPR AKKRGLPQLG TLGAGNHYAE IQVVDEIFNE
     YAAKKMGIDH KGQVCVMIHS GSRGLGHQVA TDALVAMEKA MKRDKIIVND RQLACARIAS
     PEGQDYLKGM AAAGNYAWVN RSSMTFLTRQ AFAKVFNTTP DDLDLHVIYD VSHNIAKVEQ
     HVVDGKERTL LVHRKGSTRA FPPHHPLIAV DYQLTGQPVL IGGTMGTCSY VLTGTEQGMT
     ETFGTTCHGA GRALSRAKSR RNLDFQDVLD KLADMGIAIR VASPKLVMEE APESYKNVTD
     VVNTCHDAGI SKKAIKLRPI AVIKG
//