ID A0A3P8Z991_ESOLU Unreviewed; 443 AA.
AC A0A3P8Z991;
DT 13-FEB-2019, integrated into UniProtKB/TrEMBL.
DT 13-FEB-2019, sequence version 1.
DT 27-MAR-2024, entry version 25.
DE RecName: Full=Polyribonucleotide 5'-hydroxyl-kinase Clp1 {ECO:0000256|HAMAP-Rule:MF_03035};
DE EC=2.7.1.78 {ECO:0000256|HAMAP-Rule:MF_03035};
DE AltName: Full=Polyadenylation factor Clp1 {ECO:0000256|HAMAP-Rule:MF_03035};
DE AltName: Full=Polynucleotide kinase Clp1 {ECO:0000256|HAMAP-Rule:MF_03035};
DE AltName: Full=Pre-mRNA cleavage complex II protein Clp1 {ECO:0000256|HAMAP-Rule:MF_03035};
GN Name=CLP1 {ECO:0000256|HAMAP-Rule:MF_03035};
OS Esox lucius (Northern pike).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Esociformes;
OC Esocidae; Esox.
OX NCBI_TaxID=8010 {ECO:0000313|Ensembl:ENSELUP00000025394.1, ECO:0000313|Proteomes:UP000265140};
RN [1] {ECO:0000313|Ensembl:ENSELUP00000025394.1, ECO:0000313|Proteomes:UP000265140}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=25069045;
RA Rondeau E.B., Minkley D.R., Leong J.S., Messmer A.M., Jantzen J.R.,
RA von Schalburg K.R., Lemon C., Bird N.H., Koop B.F.;
RT "The genome and linkage map of the northern pike (Esox lucius): conserved
RT synteny revealed between the salmonid sister group and the Neoteleostei.";
RL PLoS ONE 9:e102089-e102089(2014).
RN [2] {ECO:0000313|Ensembl:ENSELUP00000025394.1}
RP IDENTIFICATION.
RG Ensembl;
RL Submitted (SEP-2023) to UniProtKB.
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. Appears to have roles 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. Component of the pre-mRNA cleavage complex II (CF-II),
CC 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:0000256|HAMAP-Rule:MF_03035}.
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:0000256|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:0000256|HAMAP-
CC Rule:MF_03035};
CC -!- SUBUNIT: Component of the tRNA splicing endonuclease complex. Component
CC of pre-mRNA cleavage complex II (CF-II). {ECO:0000256|HAMAP-
CC Rule:MF_03035}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123,
CC ECO:0000256|HAMAP-Rule:MF_03035}.
CC -!- SIMILARITY: Belongs to the Clp1 family. Clp1 subfamily.
CC {ECO:0000256|HAMAP-Rule:MF_03035}.
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DR RefSeq; XP_010899913.1; XM_010901611.3.
DR RefSeq; XP_012989088.1; XM_013133634.2.
DR RefSeq; XP_012989089.1; XM_013133635.2.
DR RefSeq; XP_012989090.1; XM_013133636.2.
DR RefSeq; XP_019901518.1; XM_020045959.1.
DR AlphaFoldDB; A0A3P8Z991; -.
DR STRING; 8010.ENSELUP00000025394; -.
DR Ensembl; ENSELUT00000037071.2; ENSELUP00000025394.1; ENSELUG00000024048.2.
DR GeneID; 105028688; -.
DR KEGG; els:105028688; -.
DR GeneTree; ENSGT00940000153668; -.
DR InParanoid; A0A3P8Z991; -.
DR OMA; VQYVNCH; -.
DR OrthoDB; 56092at2759; -.
DR Proteomes; UP000265140; LG04.
DR Bgee; ENSELUG00000024048; Expressed in ovary and 15 other cell types or tissues.
DR GO; GO:0005849; C:mRNA cleavage factor complex; IEA:UniProtKB-UniRule.
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: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:0007420; P:brain development; IEA:Ensembl.
DR GO; GO:0031124; P:mRNA 3'-end processing; IEA:UniProtKB-UniRule.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0070922; P:RISC complex assembly; IEA:UniProtKB-UniRule.
DR GO; GO:0021522; P:spinal cord motor neuron differentiation; IEA:Ensembl.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IEA:UniProtKB-UniRule.
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; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_03035}; Kinase {ECO:0000256|HAMAP-Rule:MF_03035};
KW mRNA processing {ECO:0000256|ARBA:ARBA00022664, ECO:0000256|HAMAP-
KW Rule:MF_03035};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_03035};
KW Nucleus {ECO:0000256|ARBA:ARBA00023242, ECO:0000256|HAMAP-Rule:MF_03035};
KW Reference proteome {ECO:0000313|Proteomes:UP000265140};
KW Transferase {ECO:0000256|HAMAP-Rule:MF_03035};
KW tRNA processing {ECO:0000256|HAMAP-Rule:MF_03035}.
FT DOMAIN 27..117
FT /note="Clp1 N-terminal beta-sandwich"
FT /evidence="ECO:0000259|Pfam:PF16573"
FT DOMAIN 131..317
FT /note="Polyribonucleotide 5'-hydroxyl-kinase Clp1 P-loop"
FT /evidence="ECO:0000259|Pfam:PF16575"
FT DOMAIN 324..441
FT /note="Pre-mRNA cleavage complex subunit Clp1 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF06807"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 32
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03035"
FT BINDING 72
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03035"
FT BINDING 134..139
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03035"
SQ SEQUENCE 443 AA; 48410 MW; 86E9A59CDAF59013 CRC64;
MAAEGPEKTA EEGAGAGAGN GGTRYDLEKE TELRFEVDAG EKVQLELLTG LAEIFGSELN
RNKKYTFGPG SKVAVFTWQG CSVSLSGKTE VAYVSKDTPM LLYLNTHAAL EQMRRQAERD
NERGPRVMVA GPTDVGKSTV CRLLLSYAVR LGRRPTLVEL DVGQSGVSVP GTMSALCIER
PADVEEGYSV QAPLVYHFGS TSPGTNIKLY NKLTSCLADV FSQRCEVNRK ASVGGCIINT
CGWVKGSGYQ ALVHCASAFE VDVVLVLDQE RLYNELKRDL PHFVRVVLLP KSGGVVERSK
DCRREARDEK IREYFYGFRS ASFFPHAFDV RFSDVRIYKI GAPSIPDSCL PLGMSQDDTQ
LKLVPVTPGR DLTHHVLSVS CADEGEEGAG GVRRGVLESP VCGFIVVTNV DTQAQVMTVL
SPAPRPLPRH TLLIMDIRFI DLK
//
