RTCB_PAPAN
ID RTCB_PAPAN Reviewed; 505 AA.
AC A9CB42;
DT 08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 1.
DT 03-AUG-2022, entry version 70.
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};
GN Name=RTCB {ECO:0000255|HAMAP-Rule:MF_03144};
OS Papio anubis (Olive baboon).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini;
OC Cercopithecidae; Cercopithecinae; Papio.
OX NCBI_TaxID=9555;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Antonellis A., Benjamin B., Blakesley R.W., Bouffard G.G., Brinkley C.,
RA Brooks S., Chu G., Chub I., Coleman H., Fuksenko T., Gestole M.,
RA Gregory M., Guan X., Gupta J., Gurson N., Han E., Han J., Hansen N.,
RA Hargrove A., Hines-Harris K., Ho S.-L., Hu P., Hunter G., Hurle B.,
RA Idol J.R., Johnson T., Knight E., Kwong P., Lee-Lin S.-Q., Legaspi R.,
RA Madden M., Maduro Q.L., Maduro V.B., Margulies E.H., Masiello C.,
RA Maskeri B., McDowell J., Merkulov G., Montemayor C., Mullikin J.C.,
RA Park M., Prasad A., Ramsahoye C., Reddix-Dugue N., Riebow N., Schandler K.,
RA Schueler M.G., Sison C., Smith L., Stantripop S., Thomas J.W., Thomas P.J.,
RA Tsipouri V., Young A., Green E.D.;
RT "NISC comparative sequencing initiative.";
RL Submitted (NOV-2007) to the EMBL/GenBank/DDBJ databases.
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; DP000487; ABW96826.1; -; Genomic_DNA.
DR RefSeq; NP_001162246.1; NM_001168775.1.
DR AlphaFoldDB; A9CB42; -.
DR SMR; A9CB42; -.
DR STRING; 9555.ENSPANP00000013203; -.
DR Ensembl; ENSPANT00000008987; ENSPANP00000013203; ENSPANG00000016035.
DR GeneID; 100137237; -.
DR KEGG; panu:100137237; -.
DR CTD; 51493; -.
DR eggNOG; KOG3833; Eukaryota.
DR GeneTree; ENSGT00940000155911; -.
DR HOGENOM; CLU_022279_0_0_1; -.
DR OMA; QTRGVEC; -.
DR OrthoDB; 394775at2759; -.
DR Proteomes; UP000028761; Chromosome 16.
DR Bgee; ENSPANG00000016035; Expressed in cornea and 67 other tissues.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005829; C:cytosol; IEA:Ensembl.
DR GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
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; IEA:Ensembl.
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 3: Inferred from homology;
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_0000328510"
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"
SQ SEQUENCE 505 AA; 55200 MW; 173F91DE5D81CDCB CRC64;
MSRNYNDELQ FLEKISKNCW RIKKGFVPNM QVEGVFYVND ALEKLMFEEL RNACRGGGVG
GFLPAMKQIG NVAALPGIVH RSIGLPDVHS GYGFAIGNMA AFDMNDSEAV VSPGGVGFDI
NCGVRLLRTN LDESDVQPVK EQLAQAMFDH IPVGVGSKGV IPMNAKDLEE ALEMGVDWSL
REGYAWAEDK EHCEEYGRML QADPNKVSAR 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
