CLP1_DANRE
ID CLP1_DANRE Reviewed; 443 AA.
AC E7F3I6;
DT 11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT 08-MAR-2011, sequence version 1.
DT 03-AUG-2022, entry version 71.
DE RecName: Full=Polyribonucleotide 5'-hydroxyl-kinase Clp1;
DE EC=2.7.1.78;
DE AltName: Full=Polyadenylation factor Clp1;
DE AltName: Full=Polynucleotide kinase Clp1;
DE AltName: Full=Pre-mRNA cleavage complex II protein Clp1;
GN Name=clp1;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP FUNCTION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP LEU-35.
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 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. Its role in tRNA splicing and maturation is required for
CC cerebellar development. Component of the pre-mRNA cleavage complex II
CC (CF-II), which seems to be required for mRNA 3'-end formation. Also
CC phosphorylates the 5'-terminus of exogenously introduced short
CC interfering RNAs (siRNAs), which is a necessary prerequisite for their
CC incorporation into the RNA-induced silencing complex (RISC). However,
CC endogenous siRNAs and microRNAs (miRNAs) that are produced by the
CC cleavage of dsRNA precursors by dicer1 already contain a 5'-phosphate
CC group, so this protein may be dispensible for normal RNA-mediated gene
CC silencing. {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 -!- 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;
CC -!- SUBUNIT: Component of the tRNA splicing endonuclease complex. Component
CC of pre-mRNA cleavage complex II (CF-II) (By similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Strong neural expression.
CC {ECO:0000269|PubMed:24766810}.
CC -!- DISRUPTION PHENOTYPE: Lethality before 5 days post-fertilization (dpf).
CC Mutants display abnormal swimming behavior, abnormal head shape and
CC curved tail. Defects are due to neuromotor defects and cerebellar
CC neurodegeneration. {ECO:0000269|PubMed:24766810}.
CC -!- SIMILARITY: Belongs to the Clp1 family. Clp1 subfamily. {ECO:0000305}.
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; CR855307; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_001333167.1; NM_001346238.1.
DR AlphaFoldDB; E7F3I6; -.
DR SMR; E7F3I6; -.
DR STRING; 7955.ENSDARP00000087664; -.
DR PaxDb; E7F3I6; -.
DR PeptideAtlas; E7F3I6; -.
DR Ensembl; ENSDART00000093232; ENSDARP00000087664; ENSDARG00000063663.
DR GeneID; 565621; -.
DR KEGG; dre:565621; -.
DR CTD; 10978; -.
DR ZFIN; ZDB-GENE-030131-5306; clp1.
DR eggNOG; KOG2749; Eukaryota.
DR GeneTree; ENSGT00940000153668; -.
DR HOGENOM; CLU_018195_1_0_1; -.
DR InParanoid; E7F3I6; -.
DR OMA; VQYVNCH; -.
DR OrthoDB; 814241at2759; -.
DR PhylomeDB; E7F3I6; -.
DR TreeFam; TF105795; -.
DR Reactome; R-DRE-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-DRE-72187; mRNA 3'-end processing.
DR Reactome; R-DRE-73856; RNA Polymerase II Transcription Termination.
DR Reactome; R-DRE-77595; Processing of Intronless Pre-mRNAs.
DR PRO; PR:E7F3I6; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 14.
DR Bgee; ENSDARG00000063663; Expressed in early embryo and 23 other tissues.
DR GO; GO:0005849; C:mRNA cleavage factor complex; IEA:UniProtKB-UniRule.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000214; C:tRNA-intron endonuclease complex; IEA:UniProtKB-UniRule.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046404; F:polydeoxyribonucleotide 5'-hydroxyl-kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0051731; F:polynucleotide 5'-hydroxyl-kinase activity; IBA:GO_Central.
DR GO; GO:0051736; F:polyribonucleotide 5'-hydroxyl-kinase activity; IMP:UniProtKB.
DR GO; GO:0007420; P:brain development; IMP:ZFIN.
DR GO; GO:0021695; P:cerebellar cortex development; ISS:UniProtKB.
DR GO; GO:0006378; P:mRNA polyadenylation; IBA:GO_Central.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006396; P:RNA processing; IBA:GO_Central.
DR GO; GO:0021522; P:spinal cord motor neuron differentiation; IMP:ZFIN.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; ISS:UniProtKB.
DR Gene3D; 2.40.30.330; -; 1.
DR Gene3D; 2.60.120.1030; -; 1.
DR Gene3D; 3.40.50.300; -; 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; PTHR12755; 1.
DR Pfam; PF06807; Clp1; 1.
DR Pfam; PF16573; CLP1_N; 1.
DR Pfam; PF16575; CLP1_P; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Kinase; mRNA processing; Neurodegeneration;
KW Nucleotide-binding; Nucleus; Reference proteome; Transferase;
KW tRNA processing.
FT CHAIN 1..443
FT /note="Polyribonucleotide 5'-hydroxyl-kinase Clp1"
FT /id="PRO_0000429474"
FT REGION 1..27
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 12..26
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 34
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 74
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MUTAGEN 35
FT /note="L->R: Lethality before 5 days post-fertilization
FT (dpf)."
FT /evidence="ECO:0000269|PubMed:24766810"
SQ SEQUENCE 443 AA; 48574 MW; 508AF883018EF5FE CRC64;
MTAEAAEKSV EEGLSSSGSA GSSGTRFDLD KETELRFEVE AGERVQLELL SGLAEIFGSE
LNRNKKYTFG PGSKIAVFTW QGCGVALSGK TEVAYVSKDT PMLLYLNTHA ALEQMRRQAE
KDNERGPRVM VVGPTDVGKS TVCRMLLNYA VRLGRRPTLV ELDVGQSSVS VPGTMSALCI
ERPADVEEGF SVQAPLVFHF GSTTPGTNIK LYNKLTSSLA DAFSQRCEVN RRASVGGCII
NTCGWVKGSG YQALVHCASA FQVDVVLVLD QERLYNELKR DLPHFVRVVL LPKSGGVVER
SKDCRRETRD EKIREYFYGF RGTSFYPHAF DVRFSDVRIY KIGAPSIPDS CLPLGMSQDD
TQLKLVPVSP GRDLTHHVLS VSSVDDEAEV GQSRGILESP ACGFIVVTAV DTQAQVMTVL
SPAPRPLPRH TLLIMDIRFI DLK
