AC   MF_03035;
DC   Protein; auto
TR   HAMAP; MF_03035; -; 1; level=0
XX
Names: Clp1
XX
ID   CLP1
case <OC:Vertebrata>
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;
else case <OC:Fungi>
DE   RecName: Full=mRNA cleavage and polyadenylation factor <gene_name>;
else case <OC:Caenorhabditis>
DE   RecName: Full=Protein clpf-1;
else
DE   RecName: Full=Protein CLP1 homolog;
end case
case <OC:Vertebrata> or <OC:Fungi>
GN   Name=CLP1;
else case <OC:Caenorhabditis>
GN   Name=clpf-1;
end case
XX
case <OC:Vertebrata>
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 @gn(DICER1) already contain a 5'-
CC       phosphate group, so this protein may be dispensible for normal RNA-
CC       mediated gene silencing.
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   -!- 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;
else case <OC:Saccharomyces>
CC   -!- FUNCTION: Component of the cleavage factor IA (CF IA) complex, which is
CC       involved in the endonucleolytic cleavage during polyadenylation-
CC       dependent pre-mRNA 3'-end formation. Associates with HRB1/CF IB to form
CC       the cleavage factor I (CF I) complex. CF I is required for correct
CC       positioning of a larger protein complex, the cleavage and
CC       polyadenylation factor (CPF) complex, which contains the catalytic
CC       subunits executing mRNA cleavage and polyadenylation. CLP1 mediates
CC       interactions between CF IA and CPF factors. CLP1 is also involved in
CC       maintaining the CF IA interaction with the C-terminal domain of RNA Pol
CC       II largest subunit via PCF11, which links pre-mRNA 3'-end processing to
CC       transcription termination.
else
CC   -!- FUNCTION: Required for endonucleolytic cleavage during polyadenylation-
CC       dependent pre-mRNA 3'-end formation.
end case
case <OC:Mammalia>
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC       Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
end case
case <OC:Mammalia>
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.
else case <OC:Vertebrata>
CC   -!- SUBUNIT: Component of the tRNA splicing endonuclease complex. Component
CC       of pre-mRNA cleavage complex II (CF-II).
else case <OC:Saccharomyces>
CC   -!- SUBUNIT: Component of the cleavage factor IA (CF IA) complex, which is
CC       a heterohexameric complex with 2:2:1:1 stoichiometry of RNA14, RNA15,
CC       PCF11 and CLP1. It contains 2 copies of a RNA14-RNA15 dimer and 1 copy
CC       of CLP1-PCF11. The complex interacts with the cleavage factor HRB1/CF
CC       IB to form the cleavage factor I (CF I) complex, and binds to RNA.
CC       Interacts directly with PCF11. Interacts with the CPF components CFT1,
CC       PTA1, PFS2, YSH1 and SSU72.
else case <OC:Fungi>
CC   -!- SUBUNIT: Component of a pre-mRNA cleavage factor complex. Interacts
CC       directly with PCF11.
end case
CC   -!- SUBCELLULAR LOCATION: Nucleus.
CC   -!- SIMILARITY: Belongs to the Clp1 family. Clp1 subfamily.
case <OC:Fungi>
CC   -!- CAUTION: May lack the polyribonucleotide 5'-hydroxyl-kinase and
CC       polynucleotide 5'-hydroxyl-kinase activities that are characteristic of
CC       the human ortholog.
end case
XX
DR   Pfam; PF06807; Clp1; 1; trigger=no
XX
KW   mRNA processing
KW   Nucleus
case <FTTag:atp>
KW   ATP-binding
KW   Nucleotide-binding
end case
case <OC:Vertebrata>
KW   Kinase
KW   Transferase
KW   tRNA processing
end case
case <OC:Mammalia>
KW   Magnesium
KW   Manganese
KW   Nickel
end case
XX
GO   GO:0005524; F:ATP binding
GO   GO:0031124; P:mRNA 3'-end processing
GO   GO:0005634; C:nucleus
case <OC:Vertebrata>
GO   GO:0046404; F:ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity
GO   GO:0051736; F:ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity
GO   GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation
GO   GO:0070922; P:RISC complex assembly
end case
case <OC:Vertebrata>
GO   GO:0000214; C:tRNA-intron endonuclease complex
end case
case <OC:Vertebrata> or <OC:Fungi>
GO   GO:0005849; C:mRNA cleavage factor complex
end case
XX
FT   From: CLP1_YEAST (Q08685)
FT   BINDING         133..138
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT   Tag: atp; Condition: x-x-G-[KR]-[ST]-[STA]
FT   BINDING         33
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT   Optional; Condition: [DE]
FT   BINDING         72
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT   Optional; Condition: [KR]
XX
Size: 423-665;
Related: None;
Template: Q92989; Q08685; Q9SR06;
Scope:
 Eukaryota
Fusion:
 Nter: None
 Cter: None
Duplicate: None
Plasmid: None
Comments: None
XX
# Revision 1.18 2024/01/30
//