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RTCB_BOVIN
ID   RTCB_BOVIN              Reviewed;         505 AA.
AC   Q5E9T9;
DT   31-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT   15-MAR-2005, sequence version 1.
DT   03-AUG-2022, entry version 94.
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   Bos taurus (Bovine).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC   Bovinae; Bos.
OX   NCBI_TaxID=9913;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX   PubMed=16305752; DOI=10.1186/1471-2164-6-166;
RA   Harhay G.P., Sonstegard T.S., Keele J.W., Heaton M.P., Clawson M.L.,
RA   Snelling W.M., Wiedmann R.T., Van Tassell C.P., Smith T.P.L.;
RT   "Characterization of 954 bovine full-CDS cDNA sequences.";
RL   BMC Genomics 6:166-166(2005).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=Hereford; TISSUE=Uterus;
RG   NIH - Mammalian Gene Collection (MGC) project;
RL   Submitted (SEP-2005) 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; BT020831; AAX08848.1; -; mRNA.
DR   EMBL; BC104498; AAI04499.1; -; mRNA.
DR   RefSeq; NP_001015631.1; NM_001015631.2.
DR   AlphaFoldDB; Q5E9T9; -.
DR   SMR; Q5E9T9; -.
DR   STRING; 9913.ENSBTAP00000014699; -.
DR   PaxDb; Q5E9T9; -.
DR   PeptideAtlas; Q5E9T9; -.
DR   PRIDE; Q5E9T9; -.
DR   Ensembl; ENSBTAT00000014699; ENSBTAP00000014699; ENSBTAG00000011070.
DR   GeneID; 525106; -.
DR   KEGG; bta:525106; -.
DR   CTD; 51493; -.
DR   VEuPathDB; HostDB:ENSBTAG00000011070; -.
DR   VGNC; VGNC:34194; RTCB.
DR   eggNOG; KOG3833; Eukaryota.
DR   GeneTree; ENSGT00940000155911; -.
DR   HOGENOM; CLU_022279_0_0_1; -.
DR   InParanoid; Q5E9T9; -.
DR   OMA; QTRGVEC; -.
DR   OrthoDB; 394775at2759; -.
DR   TreeFam; TF314404; -.
DR   Proteomes; UP000009136; Chromosome 5.
DR   Bgee; ENSBTAG00000011070; Expressed in semen and 110 other tissues.
DR   GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR   GO; GO:0005829; C:cytosol; IEA:Ensembl.
DR   GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:Ensembl.
DR   GO; GO:0005635; C:nuclear envelope; 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:0001701; P:in utero embryonic development; IEA:Ensembl.
DR   GO; GO:0001890; P:placenta development; IEA:Ensembl.
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_0000255240"
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;  55199 MW;  D7B00F8321588230 CRC64;
     MSRSYNDELQ FLEKISKNCW RIKKGFVPNM QVEGVFYVND SLEKLMFEEL RNACRGGGVG
     GFLPAMKQIG NVAALPGIVH RSIGLPDVHS GYGFAIGNMA AFDMNDPEAV 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
 
 
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