ID CLP1_HUMAN Reviewed; 425 AA.
AC Q92989; B2R7J6; B4DTI8;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 24-JAN-2024, entry version 179.
DE RecName: Full=Polyribonucleotide 5'-hydroxyl-kinase Clp1 {ECO:0000255|HAMAP-Rule:MF_03035};
DE EC=2.7.1.78 {ECO:0000255|HAMAP-Rule:MF_03035};
DE AltName: Full=Polyadenylation factor Clp1 {ECO:0000255|HAMAP-Rule:MF_03035};
DE AltName: Full=Polynucleotide kinase Clp1 {ECO:0000255|HAMAP-Rule:MF_03035};
DE AltName: Full=Pre-mRNA cleavage complex II protein Clp1 {ECO:0000255|HAMAP-Rule:MF_03035};
GN Name=CLP1 {ECO:0000255|HAMAP-Rule:MF_03035}; Synonyms=HEAB;
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 [MRNA] (ISOFORM 1).
RX PubMed=8896421;
RA Tanabe S., Bohlander S.K., Vignon C.V., Espinosa R. III, Zhao N.,
RA Strissel P.L., Zeleznik-Le N.J., Rowley J.D.;
RT "AF10 is split by MLL and HEAB, a human homolog to a putative
RT Caenorhabditis elegans ATP/GTP-binding protein in an
RT invins(10;11)(p12;q23q12).";
RL Blood 88:3535-3545(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Cerebellum, and Placenta;
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Lung;
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 [5]
RP IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION AS A COMPONENT OF THE
RP PRE-MRNA CLEAVAGE COMPLEX II, ASSOCIATION WITH THE PRE-MRNA CLEAVAGE
RP COMPLEX I, AND SUBCELLULAR LOCATION.
RX PubMed=11060040; DOI=10.1093/emboj/19.21.5895;
RA de Vries H., Rueegsegger U., Huebner W., Friedlein A., Langen H.,
RA Keller W.;
RT "Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins
RT and bridges two other cleavage factors.";
RL EMBO J. 19:5895-5904(2000).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN A COMPLEX WITH
RP TSEN2; TSEN15; TSEN34 AND TSEN54, AND INTERACTION WITH CSTF2 AND SYMPK.
RX PubMed=15109492; DOI=10.1016/s0092-8674(04)00342-3;
RA Paushkin S.V., Patel M., Furia B.S., Peltz S.W., Trotta C.R.;
RT "Identification of a human endonuclease complex reveals a link between tRNA
RT splicing and pre-mRNA 3' end formation.";
RL Cell 117:311-321(2004).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY,
RP COFACTOR, IDENTIFICATION IN A COMPLEX WITH TSEN2; TSEN15; TSEN34 AND
RP TSEN54, AND MUTAGENESIS OF 127-LYS-SER-128.
RX PubMed=17495927; DOI=10.1038/nature05777;
RA Weitzer S., Martinez J.;
RT "The human RNA kinase hClp1 is active on 3' transfer RNA exons and short
RT interfering RNAs.";
RL Nature 447:222-226(2007).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF 127-LYS-SER-128 AND
RP ASP-151.
RX PubMed=18648070; DOI=10.1261/rna.1142908;
RA Ramirez A., Shuman S., Schwer B.;
RT "Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in
RT vivo.";
RL RNA 14:1737-1745(2008).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [10]
RP VARIANT PCH10 HIS-140, FUNCTION, IDENTIFICATION IN THE TRNA SPLICING
RP ENDONUCLEASE COMPLEX, MUTAGENESIS OF LYS-127, AND CHARACTERIZATION OF
RP VARIANT PCH10 HIS-140.
RX PubMed=24766809; DOI=10.1016/j.cell.2014.02.058;
RG Baylor Hopkins Center for Mendelian Genomics;
RA Karaca E., Weitzer S., Pehlivan D., Shiraishi H., Gogakos T., Hanada T.,
RA Jhangiani S.N., Wiszniewski W., Withers M., Campbell I.M., Erdin S.,
RA Isikay S., Franco L.M., Gonzaga-Jauregui C., Gambin T., Gelowani V.,
RA Hunter J.V., Yesil G., Koparir E., Yilmaz S., Brown M., Briskin D.,
RA Hafner M., Morozov P., Farazi T.A., Bernreuther C., Glatzel M.,
RA Trattnig S., Friske J., Kronnerwetter C., Bainbridge M.N., Gezdirici A.,
RA Seven M., Muzny D.M., Boerwinkle E., Ozen M., Clausen T., Tuschl T.,
RA Yuksel A., Hess A., Gibbs R.A., Martinez J., Penninger J.M., Lupski J.R.;
RT "Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and
RT central nervous system function.";
RL Cell 157:636-650(2014).
RN [11]
RP VARIANT PCH10 HIS-140, FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=24766810; DOI=10.1016/j.cell.2014.03.049;
RA Schaffer A.E., Eggens V.R., Caglayan A.O., Reuter M.S., Scott E.,
RA Coufal N.G., Silhavy J.L., Xue Y., Kayserili H., Yasuno K., Rosti R.O.,
RA Abdellateef M., Caglar C., Kasher P.R., Cazemier J.L., Weterman M.A.,
RA Cantagrel V., Cai N., Zweier C., Altunoglu U., Satkin N.B., Aktar F.,
RA Tuysuz B., Yalcinkaya C., Caksen H., Bilguvar K., Fu X.D., Trotta C.R.,
RA Gabriel S., Reis A., Gunel M., Baas F., Gleeson J.G.;
RT "CLP1 founder mutation links tRNA splicing and maturation to cerebellar
RT development and neurodegeneration.";
RL Cell 157:651-663(2014).
CC -!- FUNCTION: Polynucleotide kinase that can phosphorylate the 5'-hydroxyl
CC groups of double-stranded RNA (dsRNA), single-stranded RNA (ssRNA),
CC double-stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA
CC is phosphorylated more efficiently than dsDNA, and the RNA component of
CC a DNA:RNA hybrid is phosphorylated more efficiently than the DNA
CC component. Plays a key role in both tRNA splicing and mRNA 3'-end
CC formation. Component of the tRNA splicing endonuclease complex:
CC phosphorylates the 5'-terminus of the tRNA 3'-exon during tRNA
CC splicing; this phosphorylation event is a prerequisite for the
CC subsequent ligation of the two exon halves and the production of a
CC mature tRNA (PubMed:24766809, PubMed:24766810). Its role in tRNA
CC splicing and maturation is required for cerebellar development
CC (PubMed:24766809, PubMed:24766810). Component of the pre-mRNA cleavage
CC complex II (CF-II), which seems to be required for mRNA 3'-end
CC formation. Also phosphorylates the 5'-terminus of exogenously
CC introduced short interfering RNAs (siRNAs), which is a necessary
CC prerequisite for their incorporation into the RNA-induced silencing
CC complex (RISC). However, endogenous siRNAs and microRNAs (miRNAs) that
CC are produced by the cleavage of dsRNA precursors by DICER1 already
CC contain a 5'-phosphate group, so this protein may be dispensible for
CC normal RNA-mediated gene silencing. {ECO:0000269|PubMed:17495927,
CC ECO:0000269|PubMed:18648070, ECO:0000269|PubMed:24766809,
CC ECO:0000269|PubMed:24766810}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP = a 5'-end
CC 5'-monophospho-2'-deoxyribonucleoside-DNA + ADP + H(+);
CC Xref=Rhea:RHEA:15669, Rhea:RHEA-COMP:13180, Rhea:RHEA-COMP:13184,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:136412,
CC ChEBI:CHEBI:136416, ChEBI:CHEBI:456216; EC=2.7.1.78;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03035};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end dephospho-ribonucleoside-RNA + ATP = a 5'-end 5'-
CC monophospho-ribonucleoside-RNA + ADP + H(+); Xref=Rhea:RHEA:54580,
CC Rhea:RHEA-COMP:13935, Rhea:RHEA-COMP:13936, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:138282, ChEBI:CHEBI:138284,
CC ChEBI:CHEBI:456216; EC=2.7.1.78; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03035};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03035,
CC ECO:0000269|PubMed:17495927};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03035,
CC ECO:0000269|PubMed:17495927};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03035,
CC ECO:0000269|PubMed:17495927};
CC -!- SUBUNIT: Component of the tRNA splicing endonuclease complex, composed
CC of CLP1, TSEN2, TSEN15, TSEN34 and TSEN54 (PubMed:24766809). Component
CC of pre-mRNA cleavage complex II (CF-II). Also associates with numerous
CC components of the pre-mRNA cleavage complex I (CF-I/CFIm), including
CC NUDT21, CPSF2, CPSF3, CPSF6 and CPSF7. Interacts with CSTF2 and SYMPK.
CC {ECO:0000269|PubMed:15109492, ECO:0000269|PubMed:17495927,
CC ECO:0000269|PubMed:24766809}.
CC -!- INTERACTION:
CC Q92989; Q9UPV0: CEP164; NbExp=3; IntAct=EBI-2559831, EBI-3937015;
CC Q92989; Q8NCG7: DAGLB; NbExp=3; IntAct=EBI-2559831, EBI-721948;
CC Q92989; O43320: FGF16; NbExp=3; IntAct=EBI-2559831, EBI-11479104;
CC Q92989; Q9C0B1-2: FTO; NbExp=3; IntAct=EBI-2559831, EBI-18138793;
CC Q92989; Q6FHY5: MEOX2; NbExp=3; IntAct=EBI-2559831, EBI-16439278;
CC Q92989; Q14696: MESD; NbExp=3; IntAct=EBI-2559831, EBI-6165891;
CC Q92989; P22061-2: PCMT1; NbExp=3; IntAct=EBI-2559831, EBI-12386584;
CC Q92989; P79522: PRR3; NbExp=3; IntAct=EBI-2559831, EBI-2803328;
CC Q92989; P28074: PSMB5; NbExp=3; IntAct=EBI-2559831, EBI-357828;
CC Q92989; Q96H20: SNF8; NbExp=3; IntAct=EBI-2559831, EBI-747719;
CC Q92989; Q7Z6J9: TSEN54; NbExp=5; IntAct=EBI-2559831, EBI-2559824;
CC Q92989; P13994: YJU2B; NbExp=3; IntAct=EBI-2559831, EBI-716093;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03035,
CC ECO:0000269|PubMed:11060040, ECO:0000269|PubMed:24766810}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q92989-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q92989-2; Sequence=VSP_041164;
CC -!- DISEASE: Pontocerebellar hypoplasia 10 (PCH10) [MIM:615803]: A form of
CC pontocerebellar hypoplasia, a disorder characterized by structural
CC defects of the pons and cerebellum, evident upon brain imaging. PCH10
CC features include cortical dysgenesis marked by a simplified gyral
CC pattern, cortical atrophy, mild or focal cerebellar vermian volume
CC loss, delayed myelination, progressive microcephaly, global growth and
CC developmental delays, severe intellectual disabilities, and seizures
CC refractory to treatment. {ECO:0000269|PubMed:24766809,
CC ECO:0000269|PubMed:24766810}. Note=The disease is caused by variants
CC affecting the gene represented in this entry. Neurodegeneration is due
CC to defects in tRNA splicing (PubMed:24766809, PubMed:24766810).
CC {ECO:0000269|PubMed:24766809, ECO:0000269|PubMed:24766810}.
CC -!- SIMILARITY: Belongs to the Clp1 family. Clp1 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_03035}.
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DR EMBL; U73524; AAC50780.1; -; mRNA.
DR EMBL; AK300232; BAG62000.1; -; mRNA.
DR EMBL; AK313007; BAG35843.1; -; mRNA.
DR EMBL; CH471076; EAW73770.1; -; Genomic_DNA.
DR EMBL; BC000446; AAH00446.1; -; mRNA.
DR CCDS; CCDS44600.1; -. [Q92989-2]
DR CCDS; CCDS7964.1; -. [Q92989-1]
DR RefSeq; NP_001136069.1; NM_001142597.1. [Q92989-2]
DR RefSeq; NP_006822.1; NM_006831.2. [Q92989-1]
DR PDB; 8HMY; EM; 2.94 A; E=1-425.
DR PDB; 8HMZ; EM; 2.90 A; E=1-425.
DR PDBsum; 8HMY; -.
DR PDBsum; 8HMZ; -.
DR AlphaFoldDB; Q92989; -.
DR SMR; Q92989; -.
DR BioGRID; 116174; 80.
DR ComplexPortal; CPX-2692; pre-mRNA cleavage factor IIm complex.
DR ComplexPortal; CPX-2707; tRNA-intron splicing endonuclease complex.
DR CORUM; Q92989; -.
DR IntAct; Q92989; 26.
DR MINT; Q92989; -.
DR STRING; 9606.ENSP00000434995; -.
DR iPTMnet; Q92989; -.
DR MetOSite; Q92989; -.
DR PhosphoSitePlus; Q92989; -.
DR BioMuta; CLP1; -.
DR DMDM; 13431366; -.
DR EPD; Q92989; -.
DR jPOST; Q92989; -.
DR MassIVE; Q92989; -.
DR MaxQB; Q92989; -.
DR PaxDb; 9606-ENSP00000434995; -.
DR PeptideAtlas; Q92989; -.
DR ProteomicsDB; 75650; -. [Q92989-1]
DR ProteomicsDB; 75651; -. [Q92989-2]
DR Pumba; Q92989; -.
DR Antibodypedia; 27467; 220 antibodies from 28 providers.
DR DNASU; 10978; -.
DR Ensembl; ENST00000302731.4; ENSP00000304704.4; ENSG00000172409.7. [Q92989-2]
DR Ensembl; ENST00000525602.1; ENSP00000436066.1; ENSG00000172409.7. [Q92989-1]
DR Ensembl; ENST00000533682.2; ENSP00000434995.1; ENSG00000172409.7. [Q92989-1]
DR Ensembl; ENST00000681650.1; ENSP00000506714.1; ENSG00000172409.7. [Q92989-1]
DR GeneID; 10978; -.
DR KEGG; hsa:10978; -.
DR MANE-Select; ENST00000533682.2; ENSP00000434995.1; NM_006831.3; NP_006822.1.
DR UCSC; uc001nkw.4; human. [Q92989-1]
DR AGR; HGNC:16999; -.
DR CTD; 10978; -.
DR DisGeNET; 10978; -.
DR GeneCards; CLP1; -.
DR HGNC; HGNC:16999; CLP1.
DR HPA; ENSG00000172409; Low tissue specificity.
DR MalaCards; CLP1; -.
DR MIM; 608757; gene.
DR MIM; 615803; phenotype.
DR neXtProt; NX_Q92989; -.
DR OpenTargets; ENSG00000172409; -.
DR Orphanet; 411493; Pontocerebellar hypoplasia type 10.
DR PharmGKB; PA162382477; -.
DR VEuPathDB; HostDB:ENSG00000172409; -.
DR eggNOG; KOG2749; Eukaryota.
DR GeneTree; ENSGT00940000153668; -.
DR HOGENOM; CLU_018195_1_0_1; -.
DR InParanoid; Q92989; -.
DR OrthoDB; 56092at2759; -.
DR PhylomeDB; Q92989; -.
DR TreeFam; TF105795; -.
DR BRENDA; 2.7.1.78; 2681.
DR PathwayCommons; Q92989; -.
DR Reactome; R-HSA-6784531; tRNA processing in the nucleus.
DR Reactome; R-HSA-72187; mRNA 3'-end processing.
DR Reactome; R-HSA-72203; Processing of Capped Intron-Containing Pre-mRNA.
DR Reactome; R-HSA-73856; RNA Polymerase II Transcription Termination.
DR Reactome; R-HSA-77595; Processing of Intronless Pre-mRNAs.
DR SignaLink; Q92989; -.
DR SIGNOR; Q92989; -.
DR BioGRID-ORCS; 10978; 799 hits in 1163 CRISPR screens.
DR ChiTaRS; CLP1; human.
DR GenomeRNAi; 10978; -.
DR Pharos; Q92989; Tbio.
DR PRO; PR:Q92989; -.
DR Proteomes; UP000005640; Chromosome 11.
DR RNAct; Q92989; Protein.
DR Bgee; ENSG00000172409; Expressed in secondary oocyte and 194 other cell types or tissues.
DR ExpressionAtlas; Q92989; baseline and differential.
DR Genevisible; Q92989; HS.
DR GO; GO:0005829; C:cytosol; IDA:HPA.
DR GO; GO:0005849; C:mRNA cleavage factor complex; IEA:UniProtKB-UniRule.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0000214; C:tRNA-intron endonuclease complex; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; TAS:UniProtKB.
DR GO; GO:0046404; F:ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity; IDA:GO_Central.
DR GO; GO:0051736; F:ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity; IDA:GO_Central.
DR GO; GO:0051731; F:polynucleotide 5'-hydroxyl-kinase activity; IBA:GO_Central.
DR GO; GO:0021695; P:cerebellar cortex development; IMP:UniProtKB.
DR GO; GO:0098795; P:global gene silencing by mRNA cleavage; IMP:UniProtKB.
DR GO; GO:0031124; P:mRNA 3'-end processing; TAS:UniProtKB.
DR GO; GO:0006378; P:mRNA polyadenylation; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0070922; P:RISC complex assembly; IDA:UniProtKB.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IDA:UniProtKB.
DR CDD; cd01983; SIMIBI; 1.
DR Gene3D; 2.60.120.1030; Clp1, DNA binding domain; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR Gene3D; 2.40.30.330; Pre-mRNA cleavage complex subunit Clp1, C-terminal domain; 1.
DR HAMAP; MF_03035; Clp1; 1.
DR InterPro; IPR028606; Clp1.
DR InterPro; IPR045116; Clp1/Grc3.
DR InterPro; IPR010655; Clp1_C.
DR InterPro; IPR038238; Clp1_C_sf.
DR InterPro; IPR032324; Clp1_N.
DR InterPro; IPR038239; Clp1_N_sf.
DR InterPro; IPR032319; CLP1_P.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR12755; CLEAVAGE/POLYADENYLATION FACTOR IA SUBUNIT CLP1P; 1.
DR PANTHER; PTHR12755:SF6; POLYRIBONUCLEOTIDE 5'-HYDROXYL-KINASE CLP1; 1.
DR Pfam; PF06807; Clp1; 1.
DR Pfam; PF16573; CLP1_N; 1.
DR Pfam; PF16575; CLP1_P; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; ATP-binding; Disease variant; Kinase;
KW Magnesium; Manganese; mRNA processing; Neurodegeneration; Nickel;
KW Nucleotide-binding; Nucleus; Reference proteome; Transferase;
KW tRNA processing.
FT CHAIN 1..425
FT /note="Polyribonucleotide 5'-hydroxyl-kinase Clp1"
FT /id="PRO_0000089863"
FT BINDING 22
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035"
FT BINDING 62
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035"
FT BINDING 124..129
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03035"
FT VAR_SEQ 139..202
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_041164"
FT VARIANT 140
FT /note="R -> H (in PCH10; decreases kinase activity, impairs
FT formation of the tRNA splicing endonuclease complex and
FT impairs ability to mediate tRNA splicing and maturation;
FT dbSNP:rs587777616)"
FT /evidence="ECO:0000269|PubMed:24766809,
FT ECO:0000269|PubMed:24766810"
FT /id="VAR_070952"
FT MUTAGEN 127..128
FT /note="KS->AA: Abrogates RNA kinase activity. Abrogates
FT complementation of tRNA splicing activity in yeast; when
FT associated with A-128."
FT /evidence="ECO:0000269|PubMed:17495927,
FT ECO:0000269|PubMed:18648070"
FT MUTAGEN 127
FT /note="K->A: Abrogates RNA kinase activity and tRNA
FT splicing activity."
FT /evidence="ECO:0000269|PubMed:24766809"
FT MUTAGEN 151
FT /note="D->A: Abrogates complementation of tRNA splicing
FT activity in yeast."
FT /evidence="ECO:0000269|PubMed:18648070"
FT STRAND 12..17
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 19..26
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 55..57
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 62..69
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 71..77
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 80..85
FT /evidence="ECO:0007829|PDB:8HMZ"
FT HELIX 90..107
FT /evidence="ECO:0007829|PDB:8HMZ"
FT TURN 108..111
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 116..120
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 123..125
FT /evidence="ECO:0007829|PDB:8HMZ"
FT HELIX 127..140
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 146..149
FT /evidence="ECO:0007829|PDB:8HMZ"
FT TURN 152..154
FT /evidence="ECO:0007829|PDB:8HMY"
FT STRAND 156..167
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 184..187
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 190..192
FT /evidence="ECO:0007829|PDB:8HMY"
FT HELIX 193..195
FT /evidence="ECO:0007829|PDB:8HMY"
FT HELIX 197..217
FT /evidence="ECO:0007829|PDB:8HMZ"
FT HELIX 219..224
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:8HMZ"
FT HELIX 238..248
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 253..258
FT /evidence="ECO:0007829|PDB:8HMZ"
FT HELIX 260..266
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 274..279
FT /evidence="ECO:0007829|PDB:8HMZ"
FT HELIX 290..305
FT /evidence="ECO:0007829|PDB:8HMZ"
FT HELIX 308..310
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 315..320
FT /evidence="ECO:0007829|PDB:8HMZ"
FT TURN 321..323
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 325..328
FT /evidence="ECO:0007829|PDB:8HMY"
FT HELIX 359..361
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 365..369
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 383..391
FT /evidence="ECO:0007829|PDB:8HMZ"
FT TURN 394..397
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 398..405
FT /evidence="ECO:0007829|PDB:8HMZ"
FT STRAND 412..416
FT /evidence="ECO:0007829|PDB:8HMZ"
SQ SEQUENCE 425 AA; 47646 MW; 640AF4768994CFE6 CRC64;
MGEEANDDKK PTTKFELERE TELRFEVEAS QSVQLELLTG MAEIFGTELT RNKKFTFDAG
AKVAVFTWHG CSVQLSGRTE VAYVSKDTPM LLYLNTHTAL EQMRRQAEKE EERGPRVMVV
GPTDVGKSTV CRLLLNYAVR LGRRPTYVEL DVGQGSVSIP GTMGALYIER PADVEEGFSI
QAPLVYHFGS TTPGTNIKLY NKITSRLADV FNQRCEVNRR ASVSGCVINT CGWVKGSGYQ
ALVHAASAFE VDVVVVLDQE RLYNELKRDL PHFVRTVLLP KSGGVVERSK DFRRECRDER
IREYFYGFRG CFYPHAFNVK FSDVKIYKVG APTIPDSCLP LGMSQEDNQL KLVPVTPGRD
MVHHLLSVST AEGTEENLSE TSVAGFIVVT SVDLEHQVFT VLSPAPRPLP KNFLLIMDIR
FMDLK
//
