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RTCB_PYRFU
ID   RTCB_PYRFU              Reviewed;         970 AA.
AC   Q8U0H4;
DT   18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 1.
DT   03-AUG-2022, entry version 102.
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};
DE   Contains:
DE     RecName: Full=Pfu hyp2 intein;
DE              EC=3.1.-.-;
GN   Name=rtcB; OrderedLocusNames=PF1615;
OS   Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Pyrococcus.
OX   NCBI_TaxID=186497;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX   PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA   Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA   DiRuggiero J., Robb F.T.;
RT   "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT   horikoshii inferred from complete genomic sequences.";
RL   Genetics 152:1299-1305(1999).
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; AE009950; AAL81739.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q8U0H4; -.
DR   SMR; Q8U0H4; -.
DR   IntAct; Q8U0H4; 1.
DR   STRING; 186497.PF1615; -.
DR   EnsemblBacteria; AAL81739; AAL81739; PF1615.
DR   KEGG; pfu:PF1615; -.
DR   PATRIC; fig|186497.12.peg.1682; -.
DR   eggNOG; arCOG03158; Archaea.
DR   eggNOG; arCOG04246; Archaea.
DR   HOGENOM; CLU_012374_0_0_2; -.
DR   OMA; VHNCGVR; -.
DR   PhylomeDB; Q8U0H4; -.
DR   BRENDA; 6.5.1.8; 5243.
DR   Proteomes; UP000001013; Chromosome.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR   GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0008452; F:RNA ligase activity; IEA:InterPro.
DR   GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR   GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR   GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR   Gene3D; 3.10.28.10; -; 1.
DR   Gene3D; 3.90.1860.10; -; 2.
DR   InterPro; IPR003586; Hint_dom_C.
DR   InterPro; IPR003587; Hint_dom_N.
DR   InterPro; IPR036844; Hint_dom_sf.
DR   InterPro; IPR027434; Homing_endonucl.
DR   InterPro; IPR006142; INTEIN.
DR   InterPro; IPR030934; Intein_C.
DR   InterPro; IPR004042; Intein_endonuc.
DR   InterPro; IPR006141; Intein_N.
DR   InterPro; IPR004860; LAGLIDADG_2.
DR   InterPro; IPR001233; RtcB.
DR   InterPro; IPR036025; RtcB-like_sf.
DR   PANTHER; PTHR11118; PTHR11118; 1.
DR   Pfam; PF14528; LAGLIDADG_3; 1.
DR   Pfam; PF01139; RtcB; 1.
DR   PRINTS; PR00379; INTEIN.
DR   SMART; SM00305; HintC; 1.
DR   SMART; SM00306; HintN; 1.
DR   SUPFAM; SSF103365; SSF103365; 2.
DR   SUPFAM; SSF51294; SSF51294; 1.
DR   SUPFAM; SSF55608; SSF55608; 1.
DR   TIGRFAMs; TIGR01443; intein_Cterm; 1.
DR   TIGRFAMs; TIGR01445; intein_Nterm; 1.
DR   PROSITE; PS50818; INTEIN_C_TER; 1.
DR   PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1.
DR   PROSITE; PS50817; INTEIN_N_TER; 1.
PE   3: Inferred from homology;
KW   Autocatalytic cleavage; DNA-binding; Endonuclease; GTP-binding; Hydrolase;
KW   Intron homing; Ligase; Manganese; Metal-binding; Nuclease;
KW   Nucleotide-binding; Protein splicing; Reference proteome; tRNA processing.
FT   CHAIN           1..105
FT                   /note="tRNA-splicing ligase RtcB, 1st part"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000232532"
FT   CHAIN           106..586
FT                   /note="Pfu hyp2 intein"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000232533"
FT   CHAIN           587..970
FT                   /note="tRNA-splicing ligase RtcB, 2nd part"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_0000232534"
FT   DOMAIN          256..420
FT                   /note="DOD-type homing endonuclease"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00273"
FT   ACT_SITE        893
FT                   /note="GMP-histidine intermediate"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         103
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         587
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         587
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         691..695
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         692
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         723
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         818..819
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         818
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         867..870
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         874
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         893..896
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
FT   BINDING         969
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000250|UniProtKB:O59245"
SQ   SEQUENCE   970 AA;  109712 MW;  CC0AEE4573CFE7C2 CRC64;
     MIILRVVNVA VPLKRIDKIR WEIPKFDKRM KVPGRVYADD VLIEKMRQDR TLEQAANVAM
     LPGIYKYSIV MPDGHQGYGF PIGGVAAFDI KEGVISPGGI GYDINCLAPG TKVLTEHGYW
     LKIEEMPEKF KLQRLRLYNI EEGHNDFSRV AFVAERNIEK DETAIRIVTE TGTLIEGSED
     HPVLTPQGYV YLKNIKEGDY VIVYPFEGVP YEEKKGIIID ESAFEGEDPQ VIKFLKERNL
     LPLRWEDPKI GTLARILGFA LGDGHLGEMG GRLVLAFYGR EETLRELKKD LESLGIKANL
     YVREKNYRIK TESGEYSGKT VLAELRVSSR SFALLLEKLG MPRGEKTKKA YRIPVWIMEA
     PLWVKRNFLA GFFGADGSIV EFKGTTPLPI HLTQAKDVAL EENLKEFLYD ISRILEEFGV
     KTTIYKVNSK KSVTYRLSIV GEENIRNFLG KINYEYDPKK KAKGLIAYAY LKFKESVKKE
     RRKAMEISKK IYEETGNIDR AYKAVKDIVN RRFVERTIYE GERNPRVPKN FLTFEEFAKE
     RGYEGGFVAE KVVKVERIKP EYDRFYDIGV YHEAHNFIAN GIVVHNCGVR LIRTNLTEKD
     VRPKIKQLVD TLFKNVPSGV GSQGKVRLHW TQIDDVLVDG AKWAVDQGYG WERDLERLEE
     GGRMEGADPD AVSQRAKQRG APQLGSLGSG NHFLEVQVVD KIFDEEIAKA YGLFEGQVVV
     MVHTGSRGLG HQVASDYLRI MERAIRKYGI PWPDRELVSV PFQSEEGQRY FSAMKAAANF
     AWANRQMITH WVRESFQEVF RQDPEGDLGM EIVYDVAHNI GKVEEHEVDG KKVKVIVHRK
     GATRAFPPGH EAIPKIYRDV GQPVLIPGSM GTASYVLAGT EGAMAETFGS TCHGAGRVLS
     RAAATRQYRG DRIRDELLRR GIYVRAASMR VVAEEAPGAY KNVDNVVKVV SEAGIAKLVA
     RMRPIGVAKG
 
 
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