ID   CLP1_BOVIN              Reviewed;         425 AA.
AC   A2VE01;
DT   26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT   20-MAR-2007, sequence version 1.
DT   02-SEP-2026, entry version 107.
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};
OS   Bos taurus (Bovine).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC   Bovinae; Bos.
OX   NCBI_TaxID=9913;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=Hereford; TISSUE=Basal ganglia;
RG   NIH - Mammalian Gene Collection (MGC) project;
RL   Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases.
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. 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 (By similarity). {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a 5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP = a 5'-end
CC         5'-phospho-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         phospho-ribonucleoside-RNA + ADP + H(+); Xref=Rhea:RHEA:54580,
CC         Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:15179, 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; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_03035};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_03035};
CC       Name=Ni(2+); Xref=ChEBI:CHEBI:49786; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_03035};
CC   -!- SUBUNIT: Component of the tRNA splicing endonuclease complex, composed
CC       of CLP1, TSEN2, TSEN15, TSEN34 and TSEN54. Component of pre-mRNA
CC       cleavage complex II (CF-II). Also associates with numerous components
CC       of the pre-mRNA cleavage complex I (CF-I/CFIm), including NUDT21,
CC       CPSF2, CPSF3, CPSF6 and CPSF7. Interacts with CSTF2 and SYMPK.
CC       {ECO:0000255|HAMAP-Rule:MF_03035}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03035}.
CC   -!- SIMILARITY: Belongs to the Clp1 family. Clp1 subfamily.
CC       {ECO:0000255|HAMAP-Rule:MF_03035}.
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; BC133499; AAI33500.1; -; mRNA.
DR   RefSeq; NP_001075182.1; NM_001081713.1.
DR   RefSeq; XP_005216587.1; XM_005216530.5.
DR   RefSeq; XP_005216588.1; XM_005216531.5.
DR   RefSeq; XP_005216589.1; XM_005216532.5.
DR   RefSeq; XP_024830855.1; XM_024975087.2.
DR   RefSeq; XP_059730591.1; XM_059874608.1.
DR   AlphaFoldDB; A2VE01; -.
DR   SMR; A2VE01; -.
DR   FunCoup; A2VE01; 3560.
DR   STRING; 9913.ENSBTAP00000062480; -.
DR   GlyGen; A2VE01; 2 sites.
DR   PaxDb; 9913-ENSBTAP00000062480; -.
DR   Ensembl; ENSBTAT00000008507.5; ENSBTAP00000008507.3; ENSBTAG00000006493.6.
DR   Ensembl; ENSBTAT00085025407; ENSBTAP00085010675; ENSBTAG00085010459.
DR   Ensembl; ENSBTAT00090057214; ENSBTAP00090030363; ENSBTAG00090027186.
DR   GeneID; 506507; -.
DR   KEGG; bta:506507; -.
DR   CTD; 10978; -.
DR   VEuPathDB; HostDB:ENSBTAG00000006493; -.
DR   VGNC; VGNC:27457; CLP1.
DR   eggNOG; KOG2749; Eukaryota.
DR   GeneTree; ENSGT00940000153668; -.
DR   HOGENOM; CLU_018195_1_0_1; -.
DR   InParanoid; A2VE01; -.
DR   OMA; VQYVNCH; -.
DR   OrthoDB; 258143at2759; -.
DR   Reactome; R-BTA-73856; RNA Polymerase II Transcription Termination.
DR   Reactome; R-BTA-77595; Processing of Intronless Pre-mRNAs.
DR   Reactome; R-BTA-9770562; mRNA Polyadenylation.
DR   Proteomes; UP000009136; Chromosome 15.
DR   Bgee; ENSBTAG00000006493; Expressed in oocyte and 109 other cell types or tissues.
DR   GO; GO:0005849; C:mRNA cleavage factor complex; IEA:UniProtKB-UniRule.
DR   GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
DR   GO; GO:0000214; C:tRNA-intron endonuclease complex; ISS:UniProtKB.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0046404; F:ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0051736; F:ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0051731; F:polynucleotide 5'-hydroxyl-kinase activity; IBA:GO_Central.
DR   GO; GO:0021695; P:cerebellar cortex development; ISS:UniProtKB.
DR   GO; GO:0031124; P:mRNA 3'-end processing; IEA:UniProtKB-UniRule.
DR   GO; GO:0031440; P:regulation of mRNA 3'-end processing; IEA:Ensembl.
DR   GO; GO:0070922; P:RISC complex assembly; ISS:UniProtKB.
DR   GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; ISS:UniProtKB.
DR   GO; GO:0000379; P:tRNA-type intron splice site recognition and cleavage; IEA:Ensembl.
DR   CDD; cd01983; SIMIBI; 1.
DR   FunFam; 2.40.30.330:FF:000001; Protein CLP1 homolog; 1.
DR   FunFam; 3.40.50.300:FF:000454; Protein CLP1 homolog; 1.
DR   FunFam; 2.60.120.1030:FF:000001; Protein CLP1 homolog 5; 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   2: Evidence at transcript level;
KW   ATP-binding; Kinase; Magnesium; Manganese; mRNA processing; 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_0000375166"
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"
SQ   SEQUENCE   425 AA;  47630 MW;  39947D9089F6FFE8 CRC64;
     MGEEANDDKK PTTKFELERE TELRFEVEAS QSVQLELLAG MAEIFGTELT RNKKFTFDAG
     AKVAVFTWHG CSLQLSGRTE 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
//