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HAMAP rule MF_03035

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General rule information [?]

Accession MF_03035
Dates 21-APR-2009 (Created)
30-JAN-2024 (Last updated, Version 18)
Name Clp1
Scope(s) Eukaryota
Template(s) Q92989 (CLP1_HUMAN); Q08685 (CLP1_YEAST); Q9SR06 (CLP1_ARATH); [ Recover all ]
Triggered by HAMAP; MF_03035 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier CLP1
case <OC:Vertebrata>
Protein name RecName: Full=Polyribonucleotide 5'-hydroxyl-kinase Clp1;
AltName: Full=Polyadenylation factor Clp1;
AltName: Full=Polynucleotide kinase Clp1;
AltName: Full=Pre-mRNA cleavage complex II protein Clp1;
else case <OC:Fungi>
Protein name RecName: Full=mRNA cleavage and polyadenylation factor ;
else case <OC:Caenorhabditis>
Protein name RecName: Full=Protein clpf-1;
Protein name RecName: Full=Protein CLP1 homolog;
end case
case <OC:Vertebrata> or <OC:Fungi>
Gene name Name=CLP1;
else case <OC:Caenorhabditis>
Gene name Name=clpf-1;
end case

Comments [?]

case <OC:Vertebrata>
FUNCTIONPolynucleotide kinase that can phosphorylate the 5'-hydroxyl groups of double-stranded RNA (dsRNA), single-stranded RNA (ssRNA), double stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA is phosphorylated more efficiently than dsDNA, and the RNA component of a DNA:RNA hybrid is phosphorylated more efficiently than the DNA component. Appears to have roles in both tRNA splicing and mRNA 3'-end formation. Component of the tRNA splicing endonuclease complex. Phosphorylates the 5'-terminus of the tRNA 3'-exon during tRNA splicing; this phosphorylation event is a prerequisite for the subsequent ligation of the two exon halves and the production of a mature tRNA. Component of the pre-mRNA cleavage complex II (CF-II), which seems to be required for mRNA 3'-end formation. Also phosphorylates the 5'-terminus of exogenously introduced short interfering RNAs (siRNAs), which is a necessary prerequisite for their incorporation into the RNA-induced silencing complex (RISC). However, endogenous siRNAs and microRNAs (miRNAs) that are produced by the cleavage of dsRNA precursors by @gn(DICER1) already contain a 5'- phosphate group, so this protein may be dispensible for normal RNA- mediated gene silencing.
CATALYTIC ACTIVITY Reaction=a 5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP = a 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA + ADP + H(+); Xref=Rhea:RHEA:15669, Rhea:RHEA-COMP:13180, Rhea:RHEA-COMP:13184, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:136412, ChEBI:CHEBI:136416, ChEBI:CHEBI:456216; EC=;
CATALYTIC ACTIVITY Reaction=a 5'-end dephospho-ribonucleoside-RNA + ATP = a 5'-end 5'- phospho-ribonucleoside-RNA + ADP + H(+); Xref=Rhea:RHEA:54580, Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:15179, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:138282, ChEBI:CHEBI:138284, ChEBI:CHEBI:456216; EC=;
else case <OC:Saccharomyces>
FUNCTIONComponent of the cleavage factor IA (CF IA) complex, which is involved in the endonucleolytic cleavage during polyadenylation- dependent pre-mRNA 3'-end formation. Associates with HRB1/CF IB to form the cleavage factor I (CF I) complex. CF I is required for correct positioning of a larger protein complex, the cleavage and polyadenylation factor (CPF) complex, which contains the catalytic subunits executing mRNA cleavage and polyadenylation. CLP1 mediates interactions between CF IA and CPF factors. CLP1 is also involved in maintaining the CF IA interaction with the C-terminal domain of RNA Pol II largest subunit via PCF11, which links pre-mRNA 3'-end processing to transcription termination.
FUNCTIONRequired for endonucleolytic cleavage during polyadenylation- dependent pre-mRNA 3'-end formation.
end case
case <OC:Mammalia>
COFACTOR Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
end case
case <OC:Mammalia>
SUBUNITComponent of the tRNA splicing endonuclease complex, composed of CLP1, TSEN2, TSEN15, TSEN34 and TSEN54. Component of pre-mRNA cleavage complex II (CF-II). Also associates with numerous components of the pre-mRNA cleavage complex I (CF-I/CFIm), including NUDT21, CPSF2, CPSF3, CPSF6 and CPSF7. Interacts with CSTF2 and SYMPK.
else case <OC:Vertebrata>
SUBUNITComponent of the tRNA splicing endonuclease complex. Component of pre-mRNA cleavage complex II (CF-II).
else case <OC:Saccharomyces>
SUBUNITComponent of the cleavage factor IA (CF IA) complex, which is a heterohexameric complex with 2:2:1:1 stoichiometry of RNA14, RNA15, PCF11 and CLP1. It contains 2 copies of a RNA14-RNA15 dimer and 1 copy of CLP1-PCF11. The complex interacts with the cleavage factor HRB1/CF IB to form the cleavage factor I (CF I) complex, and binds to RNA. Interacts directly with PCF11. Interacts with the CPF components CFT1, PTA1, PFS2, YSH1 and SSU72.
else case <OC:Fungi>
SUBUNITComponent of a pre-mRNA cleavage factor complex. Interacts directly with PCF11.
end case
SIMILARITYBelongs to the Clp1 family. Clp1 subfamily.
case <OC:Fungi>
CAUTIONMay lack the polyribonucleotide 5'-hydroxyl-kinase and polynucleotide 5'-hydroxyl-kinase activities that are characteristic of the human ortholog.
end case

Keywords [?]

mRNA processing
case <FTTag:atp>
end case
case <OC:Vertebrata>
tRNA processing
end case
case <OC:Mammalia>
end case

Gene Ontology [?]

GO:0005524; Molecular function:ATP binding
GO:0031124; Biological process:mRNA 3'-end processing
GO:0005634; Cellular component:nucleus
case <OCellular component:Vertebrata>
GO:0046404; Molecular function:ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity
GO:0051736; Molecular function:ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity
GO:0006388; Biological process:tRNA splicing, via endonucleolytic cleavage and ligation
GO:0070922; Biological process:RISC complex assembly
end case
case <OCellular component:Vertebrata>
GO:0000214; Cellular component:tRNA-intron endonuclease complex
end case
case <OCellular component:Vertebrata> or <OC:Fungi>
GO:0005849; Cellular component:mRNA cleavage factor complex
end case

Cross-references [?]

Pfam PF06807; Clp1; 1;

Features [?]

From: CLP1_YEAST (Q08685)
Key From To Description Tag Condition FTGroup
BINDING 133 138 /ligand="ATP"
atp x-x-G-[KR]-[ST]-[STA]
BINDING 33 33 /ligand="ATP"
BINDING 72 72 /ligand="ATP"

Additional information [?]

Size range 423-665 amino acids
Related rules None
Fusion Nter: None Cter: None

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