RTCB2_ENTHI
ID RTCB2_ENTHI Reviewed; 535 AA.
AC C4M6T2;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 07-JUL-2009, sequence version 1.
DT 03-AUG-2022, entry version 61.
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=EHI_184560;
OS Entamoeba histolytica.
OC Eukaryota; Amoebozoa; Evosea; Archamoebae; Mastigamoebida; Entamoebidae;
OC Entamoeba.
OX NCBI_TaxID=5759;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 30459 / HM-1:IMSS;
RX PubMed=15729342; DOI=10.1038/nature03291;
RA Loftus B.J., Anderson I., Davies R., Alsmark U.C., Samuelson J., Amedeo P.,
RA Roncaglia P., Berriman M., Hirt R.P., Mann B.J., Nozaki T., Suh B., Pop M.,
RA Duchene M., Ackers J., Tannich E., Leippe M., Hofer M., Bruchhaus I.,
RA Willhoeft U., Bhattacharya A., Chillingworth T., Churcher C.M., Hance Z.,
RA Harris B., Harris D., Jagels K., Moule S., Mungall K.L., Ormond D.,
RA Squares R., Whitehead S., Quail M.A., Rabbinowitsch E., Norbertczak H.,
RA Price C., Wang Z., Guillen N., Gilchrist C., Stroup S.E., Bhattacharya S.,
RA Lohia A., Foster P.G., Sicheritz-Ponten T., Weber C., Singh U.,
RA Mukherjee C., El-Sayed N.M.A., Petri W.A., Clark C.G., Embley T.M.,
RA Barrell B.G., Fraser C.M., Hall N.;
RT "The genome of the protist parasite Entamoeba histolytica.";
RL Nature 433:865-868(2005).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 30459 / HM-1:IMSS;
RA Lorenzi H., Amedeo P., Inman J., Schobel S., Caler E.;
RL Submitted (MAR-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}.
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; DS571308; EAL43408.1; -; Genomic_DNA.
DR RefSeq; XP_648794.1; XM_643702.1.
DR AlphaFoldDB; C4M6T2; -.
DR SMR; C4M6T2; -.
DR STRING; 5759.rna_EHI_184560-1; -.
DR GeneID; 3403072; -.
DR KEGG; ehi:EHI_184560; -.
DR VEuPathDB; AmoebaDB:EHI5A_116080; -.
DR VEuPathDB; AmoebaDB:EHI7A_081210; -.
DR VEuPathDB; AmoebaDB:EHI8A_072520; -.
DR VEuPathDB; AmoebaDB:EHI_184560; -.
DR VEuPathDB; AmoebaDB:KM1_136110; -.
DR eggNOG; KOG3833; Eukaryota.
DR InParanoid; C4M6T2; -.
DR OMA; PGSMGDY; -.
DR Proteomes; UP000001926; Partially assembled 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.
PE 3: Inferred from homology;
KW GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome; tRNA processing.
FT CHAIN 1..535
FT /note="RNA-splicing ligase RtcB homolog 2"
FT /id="PRO_0000407232"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 458
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 152
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 155
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 155
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 259..263
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 260
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 292
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 383..384
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 383
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 432..435
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 439
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 458..461
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 534
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
SQ SEQUENCE 535 AA; 59146 MW; 6D4BEAA4E9A2F48E CRC64;
MAKSRYSRKN KGKKLQRAQQ NTVSTEEKPE QEVETIDFNG FQIPKVYDGK FERKPMELEI
KKGFVEGMNG DAKIFCNDDL LNLLTFEMIK DISNNYPSCV RQTANAATLP GVVGSLAMPD
AHSGYGFSIG GVVAMRLDDP EAVICPGGVG FDINCGVRLI RTNLQREDIE QHKARLADEL
FKQIPSGVGT QAQIAFSPED FDSIMKEGLE FLVENGYAWE EDLNHCEEHG KIANADPSLV
SNSAKSRGYK QVGTLGSGNH YLEVQVVDEI MDVEAAKAMG ITEIGQVCIM VHCGSRGLGH
QVCQDYINLC MKSGICNPVD KQLTGVPFNS PIGQQYYSAM NCCANFAFAN RGMITYRIRQ
AFETVLRMKP KKMDMHLVYD VCHNIAKVEE HDVDNKKVQC IVHRKGATRA FPPQHPDISE
DYKEIGQPAI IGGSMGTCSY VLVGTQEGMK KSFGSTCHGA GRKMSRTKAM DNLTSKDVIN
RMKEMGIELR ITDPKLAAEE ADEAYKDVTE VVETCQAANI SKIVLRLKPL IVIKG
