RTCB_PLAYO
ID RTCB_PLAYO Reviewed; 507 AA.
AC Q7RI54;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-2003, sequence version 1.
DT 03-AUG-2022, entry version 74.
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 ORFNames=PY03776;
OS Plasmodium yoelii yoelii.
OC Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
OC Plasmodiidae; Plasmodium; Plasmodium (Vinckeia).
OX NCBI_TaxID=73239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=17XNL;
RX PubMed=12368865; DOI=10.1038/nature01099;
RA Carlton J.M., Angiuoli S.V., Suh B.B., Kooij T.W., Pertea M., Silva J.C.,
RA Ermolaeva M.D., Allen J.E., Selengut J.D., Koo H.L., Peterson J.D., Pop M.,
RA Kosack D.S., Shumway M.F., Bidwell S.L., Shallom S.J., van Aken S.E.,
RA Riedmuller S.B., Feldblyum T.V., Cho J.K., Quackenbush J., Sedegah M.,
RA Shoaibi A., Cummings L.M., Florens L., Yates J.R. III, Raine J.D.,
RA Sinden R.E., Harris M.A., Cunningham D.A., Preiser P.R., Bergman L.W.,
RA Vaidya A.B., van Lin L.H., Janse C.J., Waters A.P., Smith H.O., White O.R.,
RA Salzberg S.L., Venter J.C., Fraser C.M., Hoffman S.L., Gardner M.J.,
RA Carucci D.J.;
RT "Genome sequence and comparative analysis of the model rodent malaria
RT parasite Plasmodium yoelii yoelii.";
RL Nature 419:512-519(2002).
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; AABL01001111; EAA15543.1; -; Genomic_DNA.
DR AlphaFoldDB; Q7RI54; -.
DR SMR; Q7RI54; -.
DR STRING; 73239.Q7RI54; -.
DR EnsemblProtists; EAA15543; EAA15543; EAA15543.
DR InParanoid; Q7RI54; -.
DR OMA; QTRGVEC; -.
DR Proteomes; UP000008553; 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 Reference proteome; tRNA processing.
FT CHAIN 1..507
FT /note="RNA-splicing ligase RtcB homolog"
FT /id="PRO_0000407241"
FT ACT_SITE 430
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 121
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 124
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 124
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 228..232
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 229
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 261
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 355..356
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 355
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 404..407
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 411
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 430..433
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 506
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
SQ SEQUENCE 507 AA; 56240 MW; ADC2F00B2FB0AAC2 CRC64;
MMKHGKGEDV FKYIEKTNEK NLYRINKGLV PGMNVEGNMY VNEKLKLLID EEIKMYQLNK
SSTFLPAVIQ IANVSTLPGI VKASIALPDV HAGYGFSIGN VAAFDMNNEK AVISPGGVGF
DINCGVRLIR TNLFYNDIKD KQEELAQLLF NHIPVGVGSQ GFILCNQNNL DDALSLGMDW
SVKEGYSWIE DKLNCEDNGR SLYANSDYVS VRAKKRGITQ MGTLGAGNHY AEIQIVDEIY
DKKSAKLMGI EKKNQVCIMI HSGSRGLGHQ IATDALIEME KVMSKYKINV IDKQLACTPI
HSPEGQNYLK AMGAACNFAW INRSSMTFLA RQAFSKVFNQ SPDDLDMHVI YDVSHNIAKI
EEHFINGKVQ NLLVHRKGST RAFPPFHPLV PLDYQYCGQP ILIGGTMGTY SYVLTGTEKA
MENTFGSTCH GAGRALSRNK SRNSLSYSDV LSNLKEKNIS IRVASPKLIM EEAPESYKNV
SEVVQTCHDS GISNKAFRLR PVAVIKG
