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RTCB1_ENTHI
ID   RTCB1_ENTHI             Reviewed;         524 AA.
AC   C4M244;
DT   05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT   07-JUL-2009, sequence version 1.
DT   03-AUG-2022, entry version 59.
DE   RecName: Full=RNA-splicing ligase RtcB homolog 1 {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 1 {ECO:0000255|HAMAP-Rule:MF_03144};
GN   ORFNames=EHI_169260;
OS   Entamoeba histolytica.
OC   Eukaryota; Amoebozoa; Evosea; Archamoebae; Mastigamoebida; Entamoebidae;
OC   Entamoeba.
OX   NCBI_TaxID=5759;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 30459 / HM-1:IMSS;
RX   PubMed=15729342; DOI=10.1038/nature03291;
RA   Loftus B.J., Anderson I., Davies R., Alsmark U.C., Samuelson J., Amedeo P.,
RA   Roncaglia P., Berriman M., Hirt R.P., Mann B.J., Nozaki T., Suh B., Pop M.,
RA   Duchene M., Ackers J., Tannich E., Leippe M., Hofer M., Bruchhaus I.,
RA   Willhoeft U., Bhattacharya A., Chillingworth T., Churcher C.M., Hance Z.,
RA   Harris B., Harris D., Jagels K., Moule S., Mungall K.L., Ormond D.,
RA   Squares R., Whitehead S., Quail M.A., Rabbinowitsch E., Norbertczak H.,
RA   Price C., Wang Z., Guillen N., Gilchrist C., Stroup S.E., Bhattacharya S.,
RA   Lohia A., Foster P.G., Sicheritz-Ponten T., Weber C., Singh U.,
RA   Mukherjee C., El-Sayed N.M.A., Petri W.A., Clark C.G., Embley T.M.,
RA   Barrell B.G., Fraser C.M., Hall N.;
RT   "The genome of the protist parasite Entamoeba histolytica.";
RL   Nature 433:865-868(2005).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 30459 / HM-1:IMSS;
RA   Lorenzi H., Amedeo P., Inman J., Schobel S., Caler E.;
RL   Submitted (MAR-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   -!- 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; DS571219; EAL45814.1; -; Genomic_DNA.
DR   RefSeq; XP_651200.1; XM_646108.1.
DR   AlphaFoldDB; C4M244; -.
DR   SMR; C4M244; -.
DR   STRING; 5759.rna_EHI_169260-1; -.
DR   GeneID; 3405505; -.
DR   KEGG; ehi:EHI_169260; -.
DR   VEuPathDB; AmoebaDB:EHI5A_164830; -.
DR   VEuPathDB; AmoebaDB:EHI7A_138550; -.
DR   VEuPathDB; AmoebaDB:EHI8A_153420; -.
DR   VEuPathDB; AmoebaDB:EHI_169260; -.
DR   VEuPathDB; AmoebaDB:KM1_197480; -.
DR   eggNOG; KOG3833; Eukaryota.
DR   InParanoid; C4M244; -.
DR   OMA; QTRGVEC; -.
DR   Proteomes; UP000001926; Partially assembled WGS sequence.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0072669; C:tRNA-splicing ligase complex; IBA:GO_Central.
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   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.
PE   3: Inferred from homology;
KW   GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW   Reference proteome; tRNA processing.
FT   CHAIN           1..524
FT                   /note="RNA-splicing ligase RtcB homolog 1"
FT                   /id="PRO_0000407231"
FT   ACT_SITE        447
FT                   /note="GMP-histidine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         141
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         144
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         144
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         248..252
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         249
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         281
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         372..373
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         372
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         421..424
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         428
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         447..450
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT   BINDING         523
FT                   /ligand="GMP"
FT                   /ligand_id="ChEBI:CHEBI:58115"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
SQ   SEQUENCE   524 AA;  57600 MW;  53F634448E6E09A4 CRC64;
     MSSGYKPGKK RIIQPIQPIK KELIDFHGCQ IPKECEPYLE RTNVSLIIKK GFINGMKNDA
     EMFCNEDLFE LLMNELLNEQ PGASFSSCVR QTANVATLPG VIKSLAMPDA HSGYGFSIGG
     VAAMRLDDPN AVICPGGVGF DINCGVRLLR TNLDDKDIEP HLAELADALQ KNIPSGVGTT
     STQTLTEKEM NEIMNEGLEW LVKKGLAWKE DLVYCEENGR IINSDPHLVS QKARGRGRNQ
     LGTLGSGNHY LEIQRVDEIM DKEAAKQMGI SHIGQICIMI HCGSRGLGHQ VCQDFVDMCV
     SQSNKNEVDI QLTGVPFQSD NGQKYFKAMN AAANYAFANR GMISYHVRCT FEQVFQKSPK
     DLDMHLVYDV CHNIAKEESH LVDGKEIKCI VHRKGATRAF APLNPVIPDA YKPIGQPAII
     GGSMGTCSYM LVGTQEGMKK SFGSTCHGAG RKISRVNAMK NISSDSVVEE MKKKGIELRI
     TDPKLAAEEA DDAYKDVKEV VETCQSAGIS RIVFKLKPLI VVKG
 
 
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