RTCB_OSTTA
ID RTCB_OSTTA Reviewed; 515 AA.
AC Q00ZY2;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 14-NOV-2006, sequence version 1.
DT 03-AUG-2022, entry version 76.
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 OrderedLocusNames=Ot10g01930;
OS Ostreococcus tauri.
OC Eukaryota; Viridiplantae; Chlorophyta; Mamiellophyceae; Mamiellales;
OC Bathycoccaceae; Ostreococcus.
OX NCBI_TaxID=70448;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=OTTH0595;
RX PubMed=16868079; DOI=10.1073/pnas.0604795103;
RA Derelle E., Ferraz C., Rombauts S., Rouze P., Worden A.Z., Robbens S.,
RA Partensky F., Degroeve S., Echeynie S., Cooke R., Saeys Y., Wuyts J.,
RA Jabbari K., Bowler C., Panaud O., Piegu B., Ball S.G., Ral J.-P.,
RA Bouget F.-Y., Piganeau G., De Baets B., Picard A., Delseny M., Demaille J.,
RA Van de Peer Y., Moreau H.;
RT "Genome analysis of the smallest free-living eukaryote Ostreococcus tauri
RT unveils many unique features.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:11647-11652(2006).
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; CAID01000010; CAL56150.1; -; Genomic_DNA.
DR RefSeq; XP_003081626.1; XM_003081578.1.
DR AlphaFoldDB; Q00ZY2; -.
DR SMR; Q00ZY2; -.
DR STRING; 70448.Q00ZY2; -.
DR GeneID; 9832166; -.
DR KEGG; ota:OT_ostta10g01920; -.
DR eggNOG; KOG3833; Eukaryota.
DR InParanoid; Q00ZY2; -.
DR OMA; QTRGVEC; -.
DR OrthoDB; 394775at2759; -.
DR Proteomes; UP000009170; Chromosome 10.
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..515
FT /note="RNA-splicing ligase RtcB homolog"
FT /id="PRO_0000407237"
FT ACT_SITE 438
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 129
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 132
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 132
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 236..240
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 237
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 269
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 363..364
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 363
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 412..415
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 419
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 438..441
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 514
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
SQ SEQUENCE 515 AA; 55609 MW; 00E50CB9905D46F8 CRC64;
MAPATEAAPA RTYDDEAAYV TVDDAHRVRV ARGFVPNMRV DGVVYVNAAL RALVLEELAA
YCDATAHRGG GYSPALKQIA NVAALPGVVG ASIALPDVHS GYGFAIGNVA AFDVGDETSI
VSPGGVGFDI NCGVRLLRTN LTEAEVGPVK EALAQSLFDH IPVGVGSRGI IPTTPAALEA
VLEMGMDWSL REGYAWAEDK EHTEEYGRML NADPSKVSAR AKKRGLPQMG TLGAGNHYAE
IQVVDEIYDE FAAKKMGIDR VGQVCIMIHS GSRGLGHQVA TDSLTAMERA MERDGIEVND
RQLACARISS QEGQDYLAAM ACAANYAWVN RSSMTFLCRQ AFAKMFGKPP DELDMHVVYD
VSHNIAKFEE HMVDGEMKTL LVHRKGSTRA FPPHHPLIPV DYQYTGQPVL IGGTMGTCSY
ILTGTEKGMR DTFGSTCHGA GRARSRNKSR HVLQYEDVLE KLKTKGIAIR VASPKLVMEE
APESYKDVTE VVNTCHDAGI SKKCVKLRPI AVVKG
