RTCB_RAT
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 03-AUG-2022, entry version 110.
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;
CC Evidence={ECO:0000255|HAMAP-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; Q6AYT3; -.
DR PRIDE; Q6AYT3; -.
DR GeneID; 362855; -.
DR KEGG; rno:362855; -.
DR UCSC; RGD:1303261; rat.
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 OMA; QTRGVEC; -.
DR OrthoDB; 394775at2759; -.
DR PhylomeDB; Q6AYT3; -.
DR TreeFam; TF314404; -.
DR PRO; PR:Q6AYT3; -.
DR Proteomes; UP000002494; Chromosome 7.
DR Bgee; ENSRNOG00000004813; Expressed in jejunum and 19 other tissues.
DR Genevisible; Q6AYT3; RN.
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; -; 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; PTHR11118; 1.
DR Pfam; PF01139; RtcB; 1.
DR SUPFAM; SSF103365; SSF103365; 1.
DR PROSITE; PS01288; UPF0027; 1.
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
