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RTCB_THEKO
ID   RTCB_THEKO              Reviewed;         482 AA.
AC   Q5JCZ1;
DT   18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   15-FEB-2005, sequence version 1.
DT   03-AUG-2022, entry version 83.
DE   RecName: Full=tRNA-splicing ligase RtcB {ECO:0000250|UniProtKB:O59245};
DE            EC=6.5.1.8 {ECO:0000250|UniProtKB:O59245};
DE   AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000250|UniProtKB:O59245};
GN   Name=rtcB; OrderedLocusNames=TK0358;
OS   Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS   (Pyrococcus kodakaraensis (strain KOD1)).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
OX   NCBI_TaxID=69014;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX   PubMed=15710748; DOI=10.1101/gr.3003105;
RA   Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT   "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT   kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL   Genome Res. 15:352-363(2005).
CC   -!- FUNCTION: Essential for tRNA splicing and maturation. Acts by directly
CC       joining spliced tRNA halves to mature-sized tRNAs. Joins RNA with
CC       2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy
CC       ends. {ECO:0000250|UniProtKB:O59245}.
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:0000250|UniProtKB:O59245};
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:0000250|UniProtKB:O59245};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000250|UniProtKB:O59245};
CC       Note=Binds 2 manganese ions per subunit.
CC       {ECO:0000250|UniProtKB:O59245};
CC   -!- SUBUNIT: Monomer. {ECO:0000250|UniProtKB:O59245}.
CC   -!- MISCELLANEOUS: Ligation proceeds through 3 nucleotidyl transfer steps,
CC       with 2',3'-cyclic phosphate termini being hydrolyzed to 3'-P termini in
CC       a step that precedes 3'-P activation with GMP. In the first nucleotidyl
CC       transfer step, RtcB reacts with GTP to form a covalent RtcB-histidine-
CC       GMP intermediate with release of PPi; in the second step, the GMP
CC       moiety is transferred to the RNA 3'-P; in the third step, the 5'-OH
CC       from the opposite RNA strand attacks the activated 3'-P to form a
CC       3',5'-phosphodiester bond and release GMP.
CC       {ECO:0000250|UniProtKB:O59245}.
CC   -!- SIMILARITY: Belongs to the RtcB family. {ECO:0000305}.
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DR   EMBL; AP006878; BAD84547.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q5JCZ1; -.
DR   SMR; Q5JCZ1; -.
DR   STRING; 69014.TK0358; -.
DR   EnsemblBacteria; BAD84547; BAD84547; TK0358.
DR   KEGG; tko:TK0358; -.
DR   PATRIC; fig|69014.16.peg.355; -.
DR   eggNOG; arCOG04246; Archaea.
DR   HOGENOM; CLU_022279_0_1_2; -.
DR   InParanoid; Q5JCZ1; -.
DR   OMA; QTRGVEC; -.
DR   PhylomeDB; Q5JCZ1; -.
DR   Proteomes; UP000000536; Chromosome.
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; IBA:GO_Central.
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   Gene3D; 3.90.1860.10; -; 1.
DR   InterPro; IPR001233; RtcB.
DR   InterPro; IPR036025; RtcB-like_sf.
DR   PANTHER; PTHR11118; PTHR11118; 1.
DR   Pfam; PF01139; RtcB; 1.
DR   SUPFAM; SSF103365; SSF103365; 1.
PE   3: Inferred from homology;
KW   GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW   Reference proteome; tRNA processing.
FT   CHAIN           1..482
FT                   /note="tRNA-splicing ligase RtcB"
FT                   /id="PRO_0000232544"
FT   REGION          176..197
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        405
FT                   /note="GMP-histidine intermediate"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         97
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         100
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         100
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         204..208
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         205
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         236
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         330..331
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         330
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         379..382
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         386
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         405..408
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         481
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
SQ   SEQUENCE   482 AA;  53618 MW;  BC3D4ADC2CA948FC CRC64;
     MREMVPLKRI DKIRWEIPKF DKRMRVPGRV YADDQLIEKM KQDRTLEQAA NVAMLPGIYK
     YSIVMPDGHQ GYGFPIGGVA AFDAKEGVIS PGGVGYDINC GVRLIRTNLT KDEVRPKIKE
     LVDTLFKNVP SGLGSKGRVR LHWTQLDDVL ADGAKWAVDN GYGWERDLEH LEEGGRMEGA
     DPDAVSQKAK QRGAPQLGSL GSGNHFLEVQ YVDKVYNEEI AKAYGLFEGQ VVVMVHTGSR
     GLGHQVASDY LRIMEKANRK YGVPWPDREL VSVPFQSEEG QQYFSAMKAA ANFAWANRQM
     ITHWVRESFE EVFKRKAEDM EMEIVYDVAH NIAKLEEHEV DGKKVKVVVH RKGATRAFPA
     GHPDVPRAYR DVGQPVLIPG SMGTASYVLA GAEGSMRETF GSSCHGAGRL LSRKAATRQY
     RGDRLRNELL QRGIYVRAAS LRVVAEEAPG AYKSVDNVVQ VVHEAGIANL VARMRPMGVA
     KG
 
 
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