RTCB_TRIAD
ID RTCB_TRIAD Reviewed; 510 AA.
AC B3RID0;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 02-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 61.
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=TRIADDRAFT_18395;
OS Trichoplax adhaerens (Trichoplax reptans).
OC Eukaryota; Metazoa; Placozoa; Trichoplacidae; Trichoplax.
OX NCBI_TaxID=10228;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Grell-BS-1999;
RX PubMed=18719581; DOI=10.1038/nature07191;
RA Srivastava M., Begovic E., Chapman J., Putnam N.H., Hellsten U.,
RA Kawashima T., Kuo A., Mitros T., Salamov A., Carpenter M.L.,
RA Signorovitch A.Y., Moreno M.A., Kamm K., Grimwood J., Schmutz J.,
RA Shapiro H., Grigoriev I.V., Buss L.W., Schierwater B., Dellaporta S.L.,
RA Rokhsar D.S.;
RT "The Trichoplax genome and the nature of placozoans.";
RL Nature 454:955-960(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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; DS985241; EDV29731.1; -; Genomic_DNA.
DR RefSeq; XP_002108933.1; XM_002108897.1.
DR AlphaFoldDB; B3RID0; -.
DR SMR; B3RID0; -.
DR STRING; 10228.TriadP18395; -.
DR PRIDE; B3RID0; -.
DR EnsemblMetazoa; TriadT18395; TriadP18395; TriadG18395.
DR GeneID; 6750147; -.
DR KEGG; tad:TRIADDRAFT_18395; -.
DR CTD; 6750147; -.
DR eggNOG; KOG3833; Eukaryota.
DR HOGENOM; CLU_022279_0_0_1; -.
DR InParanoid; B3RID0; -.
DR OMA; QTRGVEC; -.
DR OrthoDB; 394775at2759; -.
DR PhylomeDB; B3RID0; -.
DR Proteomes; UP000009022; Unassembled 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.
DR PROSITE; PS01288; UPF0027; 1.
PE 3: Inferred from homology;
KW GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome; tRNA processing.
FT CHAIN 1..510
FT /note="RNA-splicing ligase RtcB homolog"
FT /id="PRO_0000407246"
FT ACT_SITE 433
FT /note="GMP-histidine intermediate"
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 127
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 127
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 231..235
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 232
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 264
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 358..359
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 358
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 407..410
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 414
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 433..436
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 509
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
SQ SEQUENCE 510 AA; 55975 MW; FF4A8012E5BE22D8 CRC64;
MERLNRNRSY QEELNFIEKI NDYSYRIKLG FVPNMKVEGL FYADLPLEHL MFEELQHFCS
CNGVGGFLPG VKQIGNVAAL PGIVGKSIGL PDIHSGYGFA IGNIAAFDVA NPKAIVSPGG
VGFDINCGVR LIRTNLHERD VNPMKETLAQ SLFDHIPVGV GSRGIIPMNA RDLDEALEMG
MDWSLREGYA WAEDKEHCEE YGRMLQADSN KISLRAKKRG LPQLGTLGAG NHYAEIQAVD
EIYDSFAAKS MGINRRGQIC IMVHSGSRGL GHQVATDALF NMEKAMIKDG INVNDRQLAC
ARIASDEGQN YLKGMAAAAN YAWVNRSSMT FLARQAFAKC FHTTPDDLDM HVIYDVSHNI
AKIEEHVVNG KLSTLLVHRK GSTRAFPPHH PLIPVDYQLT GQPVLIGGTM GTCSFVMTGT
SQGMSETYGT TCHGAGRALS RAKARRSLNY QEVLDRLNAS GISIRVASPK LVMEEAPESY
KDVTNVVETC HLAGISKKCF KLRPIAVIKG
