RTCB_PLAKH
ID RTCB_PLAKH Reviewed; 511 AA.
AC B3L4K9;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 02-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 62.
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=PKH_090290;
OS Plasmodium knowlesi (strain H).
OC Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
OC Plasmodiidae; Plasmodium; Plasmodium (Plasmodium).
OX NCBI_TaxID=5851;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=H;
RX PubMed=18843368; DOI=10.1038/nature07306;
RA Pain A., Boehme U., Berry A.E., Mungall K., Finn R.D., Jackson A.P.,
RA Mourier T., Mistry J., Pasini E.M., Aslett M.A., Balasubrammaniam S.,
RA Borgwardt K., Brooks K., Carret C., Carver T.J., Cherevach I.,
RA Chillingworth T., Clark T.G., Galinski M.R., Hall N., Harper D., Harris D.,
RA Hauser H., Ivens A., Janssen C.S., Keane T., Larke N., Lapp S., Marti M.,
RA Moule S., Meyer I.M., Ormond D., Peters N., Sanders M., Sanders S.,
RA Sargeant T.J., Simmonds M., Smith F., Squares R., Thurston S., Tivey A.R.,
RA Walker D., White B., Zuiderwijk E., Churcher C., Quail M.A., Cowman A.F.,
RA Turner C.M.R., Rajandream M.A., Kocken C.H.M., Thomas A.W., Newbold C.I.,
RA Barrell B.G., Berriman M.;
RT "The genome of the simian and human malaria parasite Plasmodium knowlesi.";
RL Nature 455:799-803(2008).
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; AM910991; CAQ39830.1; -; Genomic_DNA.
DR RefSeq; XP_002259057.1; XM_002259021.1.
DR AlphaFoldDB; B3L4K9; -.
DR SMR; B3L4K9; -.
DR STRING; 5851.B3L4K9; -.
DR EnsemblProtists; CAQ39830; CAQ39830; PKH_090290.
DR GeneID; 7320774; -.
DR KEGG; pkn:PKNH_0903300; -.
DR VEuPathDB; PlasmoDB:PKNH_0903300; -.
DR HOGENOM; CLU_022279_0_0_1; -.
DR InParanoid; B3L4K9; -.
DR OMA; QTRGVEC; -.
DR PhylomeDB; B3L4K9; -.
DR Proteomes; UP000031513; Chromosome 9.
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..511
FT /note="RNA-splicing ligase RtcB homolog"
FT /id="PRO_0000407240"
FT ACT_SITE 434
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 125
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 128
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 128
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 232..236
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 233
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 265
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 359..360
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 359
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 408..411
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 415
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 434..437
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 510
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
SQ SEQUENCE 511 AA; 56827 MW; EE51B32D601938E0 CRC64;
MKQGSRSEGA RGDIRGYIQK TGERNLYRIK KGLVPNMNVE GHMYVNDKLK HLIDDEIEMY
QLNRNSTFLP AVVQIANVST LPGIVKASIA LPDVHAGYGF SIGNVAAFDM SNEKAIISPG
GVGFDINCGV RLIRTNLFYE DIKDKQDELA QLLFNNIPVG VGSQGCILCN QDKLDEALCL
GMDWCVKEGY AWVEDKLNCE DNGRSFYADS NYVSVRAKKR GITQMGTLGA GNHYAEIQIV
DEIYDKRSAK LMGIEKKNQV CIMIHSGSRG LGHQIATDAL IEMEKSMTKY KIDVIDKQLA
CTPIHSKEGQ NYLKAMGSAC NFAWINRSSM TFLARQTFAK IFNQSPDDLD MHVIYDISHN
IAKMEDHLVD GKMKKLLVHR KGSTRAFPPF HPAVPLDYQY CGQPILIGGT MGTYSYVLTG
TDKAMETTFG STCHGAGRAL SRNKSRNTLN YMDVLQKMKE ENISIRVASP KLIMEEAPES
YKNVSEVVNT CHEAGISNKC FRLKPVAVIK G
