ID A0A4W6EQ56_LATCA Unreviewed; 419 AA.
AC A0A4W6EQ56;
DT 18-SEP-2019, integrated into UniProtKB/TrEMBL.
DT 18-SEP-2019, sequence version 1.
DT 18-JUN-2025, entry version 26.
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 Lates calcarifer (Barramundi) (Holocentrus calcarifer).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata;
OC Carangaria; Carangaria incertae sedis; Centropomidae; Lates.
OX NCBI_TaxID=8187 {ECO:0000313|Ensembl:ENSLCAP00010039707.1, ECO:0000313|Proteomes:UP000314980};
RN [1] {ECO:0000313|Proteomes:UP000314980}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Sai Rama Sridatta P.;
RL Submitted (SEP-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|Ensembl:ENSLCAP00010039707.1}
RP IDENTIFICATION.
RG Ensembl;
RL Submitted (MAR-2025) 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'-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:0000256|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: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 AlphaFoldDB; A0A4W6EQ56; -.
DR Ensembl; ENSLCAT00010040647.1; ENSLCAP00010039707.1; ENSLCAG00010018551.1.
DR GeneTree; ENSGT00940000153668; -.
DR Proteomes; UP000314980; Unassembled WGS sequence.
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:0031124; P:mRNA 3'-end processing; IEA:UniProtKB-UniRule.
DR GO; GO:0070922; P:RISC complex assembly; IEA:UniProtKB-UniRule.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IEA:UniProtKB-UniRule.
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; 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:UP000314980};
KW Transferase {ECO:0000256|HAMAP-Rule:MF_03035};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_03035}.
FT DOMAIN 25..118
FT /note="Clp1 N-terminal beta-sandwich"
FT /evidence="ECO:0000259|Pfam:PF16573"
FT DOMAIN 132..313
FT /note="Polyribonucleotide 5'-hydroxyl-kinase Clp1 P-loop"
FT /evidence="ECO:0000259|Pfam:PF16575"
FT DOMAIN 314..417
FT /note="Pre-mRNA cleavage complex subunit Clp1 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF06807"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..11
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 30
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03035"
FT BINDING 73
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03035"
FT BINDING 135..140
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03035"
SQ SEQUENCE 419 AA; 46093 MW; 781B1920CAA74919 CRC64;
MATEGVEKTT EDAPAAGKVS TRYDLEKETE LRFEVEAGEA AEQLELELLT GMAEVFGSEL
NRNKKYTFGP GSKIAVFTWQ GCSVNLYGKP EVAYVSKDTP MLLYLNTHAA LEQMRKQAER
DNERGPRVMV VGPTDVGKST VCRLLLSYAV RVGRRPTLVE LDVGQSGVSV PGTVSALCIE
RPADVEEGFS VQAPLVYHFG STTPGTNIKL YNKLTSCLAE VFSQRCEVNR KASVGGCIIN
TCGWVKGSGY QALVHCASAF QVDVVLVLDH ERLYNELKRD LPHFVRVVLL PKSGGVVERS
KECRRETRDE KIHVRIYKIG APSIPDSCLP LGMSQDDTQL KLVPVTPGRD LTYHVLSVSS
AEDGEEGARK GIVESPVCGF IVVTYVDTQA QVMKVLSPAP RPLPRHTLLI MDIRFMDMK
//
