RTCB_HUMAN
ID RTCB_HUMAN Reviewed; 505 AA.
AC Q9Y3I0; B2R6A8; Q6IAI0; Q9BWL4; Q9NTH1; Q9P037; Q9P0J3;
DT 31-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=RNA-splicing ligase RtcB homolog {ECO:0000255|HAMAP-Rule:MF_03144, ECO:0000305};
DE EC=6.5.1.8 {ECO:0000255|HAMAP-Rule:MF_03144, ECO:0000269|PubMed:24870230, ECO:0000305|PubMed:21311021};
DE AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000255|HAMAP-Rule:MF_03144, ECO:0000305};
GN Name=RTCB {ECO:0000255|HAMAP-Rule:MF_03144}; Synonyms=C22orf28;
GN ORFNames=HSPC117;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=12529303; DOI=10.1101/gr.695703;
RA Collins J.E., Goward M.E., Cole C.G., Smink L.J., Huckle E.J., Knowles S.,
RA Bye J.M., Beare D.M., Dunham I.;
RT "Reevaluating human gene annotation: a second-generation analysis of
RT chromosome 22.";
RL Genome Res. 13:27-36(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Umbilical cord blood;
RX PubMed=11042152; DOI=10.1101/gr.140200;
RA Zhang Q.-H., Ye M., Wu X.-Y., Ren S.-X., Zhao M., Zhao C.-J., Fu G.,
RA Shen Y., Fan H.-Y., Lu G., Zhong M., Xu X.-R., Han Z.-G., Zhang J.-W.,
RA Tao J., Huang Q.-H., Zhou J., Hu G.-X., Gu J., Chen S.-J., Chen Z.;
RT "Cloning and functional analysis of cDNAs with open reading frames for 300
RT previously undefined genes expressed in CD34+ hematopoietic stem/progenitor
RT cells.";
RL Genome Res. 10:1546-1560(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Adrenal gland;
RX PubMed=10931946; DOI=10.1073/pnas.160270997;
RA Hu R.-M., Han Z.-G., Song H.-D., Peng Y.-D., Huang Q.-H., Ren S.-X.,
RA Gu Y.-J., Huang C.-H., Li Y.-B., Jiang C.-L., Fu G., Zhang Q.-H., Gu B.-W.,
RA Dai M., Mao Y.-F., Gao G.-F., Rong R., Ye M., Zhou J., Xu S.-H., Gu J.,
RA Shi J.-X., Jin W.-R., Zhang C.-K., Wu T.-M., Huang G.-Y., Chen Z.,
RA Chen M.-D., Chen J.-L.;
RT "Gene expression profiling in the human hypothalamus-pituitary-adrenal axis
RT and full-length cDNA cloning.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:9543-9548(2000).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.;
RT "Cloning of human full open reading frames in Gateway(TM) system entry
RT vector (pDONR201).";
RL Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=15461802; DOI=10.1186/gb-2004-5-10-r84;
RA Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A.,
RA Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J.,
RA Beare D.M., Dunham I.;
RT "A genome annotation-driven approach to cloning the human ORFeome.";
RL Genome Biol. 5:R84.1-R84.11(2004).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Thalamus;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=10591208; DOI=10.1038/990031;
RA Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M.,
RA Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C.,
RA Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E.,
RA Bridgeman A.M., Buck D., Burgess J., Burrill W.D., Burton J., Carder C.,
RA Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G.,
RA Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V.,
RA Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M.,
RA Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A.,
RA Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C.,
RA Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E.,
RA Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F.,
RA Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M.,
RA Matthews L.H., Mccann O.T., Mcclay J., Mclaren S., McMurray A.A.,
RA Milne S.A., Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D.,
RA Phillimore B.J.C.T., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y.,
RA Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S.,
RA Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E.,
RA Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L.,
RA Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L.,
RA Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N.,
RA Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A.,
RA Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L.,
RA Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P.,
RA Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P.,
RA Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q.,
RA Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J.,
RA Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J.,
RA Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D.,
RA Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T.,
RA Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P.,
RA Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K.,
RA Nelson J., Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R.,
RA Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L.,
RA McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J.,
RA Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E.,
RA Fransson I., Tapia I., Bruder C.E., O'Brien K.P., Wilkinson P.,
RA Bodenteich A., Hartman K., Hu X., Khan A.S., Lane L., Tilahun Y.,
RA Wright H.;
RT "The DNA sequence of human chromosome 22.";
RL Nature 402:489-495(1999).
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [9]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT PHE-343.
RC TISSUE=Choriocarcinoma, and Lung carcinoma;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [10]
RP PROTEIN SEQUENCE OF 4-14; 45-51; 56-81; 141-158; 199-206; 264-279; 298-308;
RP 442-460 AND 466-476, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=Hepatoma;
RA Bienvenut W.V., Boldt K., von Kriegsheim A.F., Kolch W.;
RL Submitted (JUL-2007) to UniProtKB.
RN [11]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 309-505.
RC TISSUE=Testis;
RX PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D.,
RA Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A.,
RA Wiemann S., Schupp I.;
RT "The full-ORF clone resource of the German cDNA consortium.";
RL BMC Genomics 8:399-399(2007).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=Lymphoblast;
RX PubMed=14654843; DOI=10.1038/nature02166;
RA Andersen J.S., Wilkinson C.J., Mayor T., Mortensen P., Nigg E.A., Mann M.;
RT "Proteomic characterization of the human centrosome by protein correlation
RT profiling.";
RL Nature 426:570-574(2003).
RN [13]
RP IDENTIFICATION IN A RNA TRANSPORT COMPLEX.
RX PubMed=15312650; DOI=10.1016/j.neuron.2004.07.022;
RA Kanai Y., Dohmae N., Hirokawa N.;
RT "Kinesin transports RNA: isolation and characterization of an RNA-
RT transporting granule.";
RL Neuron 43:513-525(2004).
RN [14]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=16236267; DOI=10.1016/j.bbrc.2005.09.191;
RA Guo D., Han J., Adam B.-L., Colburn N.H., Wang M.-H., Dong Z.,
RA Eizirik D.L., She J.-X., Wang C.-Y.;
RT "Proteomic analysis of SUMO4 substrates in HEK293 cells under serum
RT starvation-induced stress.";
RL Biochem. Biophys. Res. Commun. 337:1308-1318(2005).
RN [15]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [16]
RP FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION BY MASS SPECTROMETRY,
RP IDENTIFICATION IN THE TRNA SPLICING LIGASE COMPLEX, AND MUTAGENESIS OF
RP CYS-122.
RX PubMed=21311021; DOI=10.1126/science.1197847;
RA Popow J., Englert M., Weitzer S., Schleiffer A., Mierzwa B., Mechtler K.,
RA Trowitzsch S., Will C.L., Luhrmann R., Soll D., Martinez J.;
RT "HSPC117 is the essential subunit of a human tRNA splicing ligase
RT complex.";
RL Science 331:760-764(2011).
RN [17]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-300, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma, and Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
RN [18]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [19]
RP FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, ACTIVITY REGULATION, AND
RP IDENTIFICATION IN THE TRNA SPLICING LIGASE COMPLEX.
RX PubMed=24870230; DOI=10.1038/nature13284;
RA Popow J., Jurkin J., Schleiffer A., Martinez J.;
RT "Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing
RT factors.";
RL Nature 511:104-107(2014).
RN [20]
RP SUBCELLULAR LOCATION.
RX PubMed=24608264; DOI=10.1371/journal.pone.0090957;
RA Perez-Gonzalez A., Pazo A., Navajas R., Ciordia S., Rodriguez-Frandsen A.,
RA Nieto A.;
RT "hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel
RT transcription-dependent shuttling RNA-transporting complex.";
RL PLoS ONE 9:E90957-E90957(2014).
RN [21]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25944712; DOI=10.1002/pmic.201400617;
RA Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
RA Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
RT "N-terminome analysis of the human mitochondrial proteome.";
RL Proteomics 15:2519-2524(2015).
RN [22]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-496, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
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, ECO:0000269|PubMed:21311021,
CC ECO:0000269|PubMed:24870230}.
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 ECO:0000269|PubMed:24870230, ECO:0000305|PubMed:21311021};
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 ECO:0000269|PubMed:24870230, ECO:0000305|PubMed:21311021};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:O59245,
CC ECO:0000255|HAMAP-Rule:MF_03144};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000250|UniProtKB:O59245,
CC ECO:0000255|HAMAP-Rule:MF_03144};
CC -!- ACTIVITY REGULATION: Protein archease stimulates the activity of the
CC tRNA ligase complex with high efficiency in the presence of GTP.
CC {ECO:0000269|PubMed:24870230}.
CC -!- SUBUNIT: Catalytic component of the tRNA-splicing ligase complex.
CC {ECO:0000255|HAMAP-Rule:MF_03144, ECO:0000269|PubMed:15312650,
CC ECO:0000269|PubMed:21311021, ECO:0000269|PubMed:24870230}.
CC -!- INTERACTION:
CC Q9Y3I0; Q9UKG1: APPL1; NbExp=3; IntAct=EBI-2107208, EBI-741243;
CC Q9Y3I0; Q9Y224: RTRAF; NbExp=4; IntAct=EBI-2107208, EBI-1104547;
CC Q9Y3I0; Q8IWT0: ZBTB8OS; NbExp=2; IntAct=EBI-2107208, EBI-2808825;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:24608264}. Cytoplasm
CC {ECO:0000255|HAMAP-Rule:MF_03144, ECO:0000269|PubMed:24608264}.
CC Note=Enters into the nucleus in case of active transcription while it
CC accumulates in cytosol when transcription level is low.
CC {ECO:0000269|PubMed:24608264}.
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, ECO:0000305|PubMed:24870230}.
CC -!- SIMILARITY: Belongs to the RtcB family. {ECO:0000255|HAMAP-
CC Rule:MF_03144}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF29081.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=AAF67477.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AL050255; CAB43357.1; -; mRNA.
DR EMBL; AF161466; AAF29081.1; ALT_FRAME; mRNA.
DR EMBL; AF155658; AAF67477.1; ALT_FRAME; mRNA.
DR EMBL; CR457175; CAG33456.1; -; mRNA.
DR EMBL; CR456450; CAG30336.1; -; mRNA.
DR EMBL; AK312503; BAG35405.1; -; mRNA.
DR EMBL; AL021937; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471095; EAW60021.1; -; Genomic_DNA.
DR EMBL; BC000151; AAH00151.1; -; mRNA.
DR EMBL; BC002970; AAH02970.1; -; mRNA.
DR EMBL; BC010308; AAH10308.1; -; mRNA.
DR EMBL; BC016707; AAH16707.1; -; mRNA.
DR EMBL; AL137272; CAB70670.1; -; mRNA.
DR CCDS; CCDS13905.1; -.
DR PIR; T46344; T46344.
DR RefSeq; NP_055121.1; NM_014306.4.
DR PDB; 7P3B; X-ray; 2.30 A; A/B=2-505.
DR PDBsum; 7P3B; -.
DR AlphaFoldDB; Q9Y3I0; -.
DR SMR; Q9Y3I0; -.
DR BioGRID; 119569; 269.
DR ComplexPortal; CPX-6411; tRNA-splicing ligase complex.
DR CORUM; Q9Y3I0; -.
DR DIP; DIP-46750N; -.
DR IntAct; Q9Y3I0; 78.
DR MINT; Q9Y3I0; -.
DR STRING; 9606.ENSP00000216038; -.
DR DrugBank; DB02772; Sucrose.
DR GlyGen; Q9Y3I0; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; Q9Y3I0; -.
DR MetOSite; Q9Y3I0; -.
DR PhosphoSitePlus; Q9Y3I0; -.
DR SwissPalm; Q9Y3I0; -.
DR BioMuta; RTCB; -.
DR DMDM; 74753486; -.
DR UCD-2DPAGE; Q9Y3I0; -.
DR EPD; Q9Y3I0; -.
DR jPOST; Q9Y3I0; -.
DR MassIVE; Q9Y3I0; -.
DR MaxQB; Q9Y3I0; -.
DR PaxDb; Q9Y3I0; -.
DR PeptideAtlas; Q9Y3I0; -.
DR PRIDE; Q9Y3I0; -.
DR ProteomicsDB; 86038; -.
DR Antibodypedia; 261; 230 antibodies from 29 providers.
DR DNASU; 51493; -.
DR Ensembl; ENST00000216038.6; ENSP00000216038.5; ENSG00000100220.12.
DR GeneID; 51493; -.
DR KEGG; hsa:51493; -.
DR MANE-Select; ENST00000216038.6; ENSP00000216038.5; NM_014306.5; NP_055121.1.
DR UCSC; uc003amm.3; human.
DR CTD; 51493; -.
DR DisGeNET; 51493; -.
DR GeneCards; RTCB; -.
DR HGNC; HGNC:26935; RTCB.
DR HPA; ENSG00000100220; Low tissue specificity.
DR MIM; 613901; gene.
DR neXtProt; NX_Q9Y3I0; -.
DR OpenTargets; ENSG00000100220; -.
DR PharmGKB; PA145149387; -.
DR VEuPathDB; HostDB:ENSG00000100220; -.
DR eggNOG; KOG3833; Eukaryota.
DR GeneTree; ENSGT00940000155911; -.
DR HOGENOM; CLU_022279_0_0_1; -.
DR InParanoid; Q9Y3I0; -.
DR OMA; QTRGVEC; -.
DR OrthoDB; 394775at2759; -.
DR PhylomeDB; Q9Y3I0; -.
DR TreeFam; TF314404; -.
DR BioCyc; MetaCyc:ENSG00000100220-MON; -.
DR BRENDA; 6.5.1.8; 2681.
DR PathwayCommons; Q9Y3I0; -.
DR Reactome; R-HSA-6784531; tRNA processing in the nucleus.
DR SignaLink; Q9Y3I0; -.
DR BioGRID-ORCS; 51493; 604 hits in 1058 CRISPR screens.
DR ChiTaRS; RTCB; human.
DR GenomeRNAi; 51493; -.
DR Pharos; Q9Y3I0; Tbio.
DR PRO; PR:Q9Y3I0; -.
DR Proteomes; UP000005640; Chromosome 22.
DR RNAct; Q9Y3I0; protein.
DR Bgee; ENSG00000100220; Expressed in jejunal mucosa and 214 other tissues.
DR Genevisible; Q9Y3I0; HS.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:HPA.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:Ensembl.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; IDA:HPA.
DR GO; GO:0005635; C:nuclear envelope; IEA:Ensembl.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0072669; C:tRNA-splicing ligase complex; IDA:UniProtKB.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR GO; GO:0003972; F:RNA ligase (ATP) activity; IDA:UniProtKB.
DR GO; GO:0017166; F:vinculin binding; IPI:UniProtKB.
DR GO; GO:0001701; P:in utero embryonic development; IEA:Ensembl.
DR GO; GO:0001890; P:placenta development; IEA:Ensembl.
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 GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IDA:UniProtKB.
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 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; GTP-binding;
KW Isopeptide bond; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW Nucleus; Phosphoprotein; Reference proteome; tRNA processing;
KW Ubl conjugation.
FT CHAIN 1..505
FT /note="RNA-splicing ligase RtcB homolog"
FT /id="PRO_0000255241"
FT ACT_SITE 428
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 119
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 122
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 122
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 226..230
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 227
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 259
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 353..354
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 353
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 402..405
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 409
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 428..431
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT BINDING 504
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245, ECO:0000255|HAMAP-
FT Rule:MF_03144"
FT MOD_RES 300
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT CROSSLNK 496
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT VARIANT 153
FT /note="V -> A (in dbSNP:rs11545747)"
FT /id="VAR_052485"
FT VARIANT 343
FT /note="L -> F (in dbSNP:rs17849275)"
FT /evidence="ECO:0000269|PubMed:15489334"
FT /id="VAR_028853"
FT MUTAGEN 122
FT /note="C->A: Abolishes tRNA ligase activity."
FT /evidence="ECO:0000269|PubMed:21311021"
FT CONFLICT 296
FT /note="A -> P (in Ref. 2; AAF29081)"
FT /evidence="ECO:0000305"
FT CONFLICT 303
FT /note="G -> V (in Ref. 2; AAF29081 and 3; AAF67477)"
FT /evidence="ECO:0000305"
FT CONFLICT 427
FT /note="C -> R (in Ref. 4; CAG33456)"
FT /evidence="ECO:0000305"
FT HELIX 5..9
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 12..16
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 19..22
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 40..54
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 65..73
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 82..89
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 96..103
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 123..132
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 133..136
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 137..139
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 140..150
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 165..174
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 176..181
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 187..191
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 194..197
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 204..206
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 209..215
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 216..218
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 228..238
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 240..245
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 253..260
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 263..283
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 291..293
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 301..335
FT /evidence="ECO:0007829|PDB:7P3B"
FT TURN 340..344
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 347..363
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 366..376
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 390..392
FT /evidence="ECO:0007829|PDB:7P3B"
FT TURN 393..395
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 398..402
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 409..414
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 416..422
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 423..426
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 436..439
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 445..454
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 458..462
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 464..470
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 472..474
FT /evidence="ECO:0007829|PDB:7P3B"
FT HELIX 478..487
FT /evidence="ECO:0007829|PDB:7P3B"
FT STRAND 490..504
FT /evidence="ECO:0007829|PDB:7P3B"
SQ SEQUENCE 505 AA; 55210 MW; C7C0CC2C95BDD27B CRC64;
MSRSYNDELQ FLEKINKNCW RIKKGFVPNM QVEGVFYVND ALEKLMFEEL RNACRGGGVG
GFLPAMKQIG NVAALPGIVH RSIGLPDVHS GYGFAIGNMA AFDMNDPEAV VSPGGVGFDI
NCGVRLLRTN LDESDVQPVK EQLAQAMFDH IPVGVGSKGV IPMNAKDLEE ALEMGVDWSL
REGYAWAEDK EHCEEYGRML QADPNKVSAR AKKRGLPQLG TLGAGNHYAE IQVVDEIFNE
YAAKKMGIDH KGQVCVMIHS GSRGLGHQVA TDALVAMEKA MKRDKIIVND RQLACARIAS
PEGQDYLKGM AAAGNYAWVN RSSMTFLTRQ AFAKVFNTTP DDLDLHVIYD VSHNIAKVEQ
HVVDGKERTL LVHRKGSTRA FPPHHPLIAV DYQLTGQPVL IGGTMGTCSY VLTGTEQGMT
ETFGTTCHGA GRALSRAKSR RNLDFQDVLD KLADMGIAIR VASPKLVMEE APESYKNVTD
VVNTCHDAGI SKKAIKLRPI AVIKG
