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RTCB_PIG
ID   RTCB_PIG                Reviewed;         505 AA.
AC   Q19PY3; Q19PY4;
DT   31-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT   11-JUL-2006, sequence version 1.
DT   03-AUG-2022, entry version 64.
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   Sus scrofa (Pig).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Laurasiatheria; Artiodactyla; Suina; Suidae; Sus.
OX   NCBI_TaxID=9823;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   TISSUE=Longissimus dorsi muscle;
RA   Xie H., Xiong Y., Lei M.;
RT   "Isolation, cDNA sequence analysis and tissue expression profile of one
RT   novel swine gene differentially expressed in the longissimus dorsi muscle
RT   tissues from Large white x Meishan cross combination.";
RL   Submitted (APR-2006) 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; DQ508262; ABF81975.1; -; mRNA.
DR   EMBL; DQ508263; ABF81976.1; -; mRNA.
DR   RefSeq; NP_001116458.1; NM_001122986.2.
DR   AlphaFoldDB; Q19PY3; -.
DR   SMR; Q19PY3; -.
DR   STRING; 9823.ENSSSCP00000000165; -.
DR   PaxDb; Q19PY3; -.
DR   PeptideAtlas; Q19PY3; -.
DR   PRIDE; Q19PY3; -.
DR   GeneID; 733658; -.
DR   KEGG; ssc:733658; -.
DR   CTD; 51493; -.
DR   eggNOG; KOG3833; Eukaryota.
DR   OrthoDB; 394775at2759; -.
DR   Proteomes; UP000008227; Unplaced.
DR   Proteomes; UP000314985; Unplaced.
DR   GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
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: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_0000255244"
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        23
FT                   /note="R -> K (in Ref. 1; ABF81975)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        182
FT                   /note="E -> G (in Ref. 1; ABF81975)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        328
FT                   /note="T -> N (in Ref. 1; ABF81975)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        356
FT                   /note="A -> V (in Ref. 1; ABF81975)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        365
FT                   /note="G -> R (in Ref. 1; ABF81975)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        407
FT                   /note="T -> A (in Ref. 1; ABF81975)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        457
FT                   /note="I -> T (in Ref. 1; ABF81975)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   505 AA;  55238 MW;  B27C915CF4EE921A CRC64;
     MSRSYNDELQ FLEKINKNCW RIRKGFVPNM QVEGVFYVND ALEKLMFEEL 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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