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RTCB2_ENTDS
ID   RTCB2_ENTDS             Reviewed;         524 AA.
AC   B0EIW5;
DT   05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT   26-FEB-2008, sequence version 1.
DT   03-AUG-2022, entry version 60.
DE   RecName: Full=RNA-splicing ligase RtcB homolog 2 {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 2 {ECO:0000255|HAMAP-Rule:MF_03144};
GN   ORFNames=EDI_260790;
OS   Entamoeba dispar (strain ATCC PRA-260 / SAW760).
OC   Eukaryota; Amoebozoa; Evosea; Archamoebae; Mastigamoebida; Entamoebidae;
OC   Entamoeba.
OX   NCBI_TaxID=370354;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC PRA-260 / SAW760;
RA   Lorenzi H., Inman J., Schobel S., Amedeo P., Caler E.;
RT   "Annotation of Entamoeba dispar SAW760.";
RL   Submitted (DEC-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; DS549501; EDR25533.1; -; Genomic_DNA.
DR   RefSeq; XP_001738172.1; XM_001738120.1.
DR   AlphaFoldDB; B0EIW5; -.
DR   SMR; B0EIW5; -.
DR   STRING; 46681.XP_001738172.1; -.
DR   EnsemblProtists; EDR25533; EDR25533; EDI_260790.
DR   GeneID; 5883243; -.
DR   KEGG; edi:EDI_260790; -.
DR   VEuPathDB; AmoebaDB:EDI_260790; -.
DR   eggNOG; KOG3833; Eukaryota.
DR   OMA; TRGECCR; -.
DR   OrthoDB; 394775at2759; -.
DR   Proteomes; UP000008076; Unassembled WGS sequence.
DR   GO; GO:0072669; C:tRNA-splicing ligase complex; IEA:UniProtKB-UniRule.
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; IEA:InterPro.
DR   GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IEA:UniProtKB-UniRule.
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   tRNA processing.
FT   CHAIN           1..524
FT                   /note="RNA-splicing ligase RtcB homolog 2"
FT                   /id="PRO_0000407230"
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;  57724 MW;  31EC5FA046DDE015 CRC64;
     MSSGYKPGKK RKVQPVQPIK KELVDFYGCQ IPKEYEPYLQ RTNVSLIIKK GFINGMKNDA
     EMFCNDDLFE LLMNELLNEQ PGASFSSCVR QTANVATLPG VIKSLAMPDA HSGYGFSIGG
     VAAMRLDDPN AVICPGGVGF DINCGVRLLR TNLDDKDIEP HLVELADALQ KNIPSGVGTT
     SNQTLTEKEM NEIMNEGLEW LVKKDLAWKE DLVYCEENGR IINSDPHLVS QKARGRGRNQ
     LGTLGSGNHY LEIQRVDEIM DMEAAKQMGI SHIGQICIMI HCGSRGLGHQ VCQDFVDLCV
     NQSNKNEVDI QLTGVPFQSD NGQKYFKAMN AAANYAFANR GMISYHVRCT FEQVFKKSPK
     DLDMHLVYDV CHNIAKEEIH LIDGNEIKCI VHRKGATRAF APLNPVIPDA YKPIGQPAII
     GGSMGTCSYM LVGTQEGMKK TFGSTCHGAG RKISRVKAMK DISSNSVVEE MKKKGIELRI
     TDPKLAAEEA DGAYKDVKEV VETCQSAGIS KIVFKLKPLI VVKG
 
 
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