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HAMAP rule MF_03035

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General rule information [?]

Accession MF_03035
Dates 21-APR-2009 (Created)
26-MAY-2023 (Last updated, Version 17)
Name Clp1
Scope
Eukaryota
Templates Q92989 (CLP1_HUMAN); Q08685 (CLP1_YEAST); Q9SR06 (CLP1_ARATH): [Recover all]
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

Identifier
CLP1
case <OC:Vertebrata>
Protein name
RecName: Full=Polyribonucleotide 5'-hydroxyl-kinase Clp1;
EC 2.7.1.78;
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;
else
Protein name
RecName: Full=Protein CLP1 homolog;
end case
case <OC:Vertebrata> or <OC:Fungi>
Gene name
CLP1
else case <OC:Caenorhabditis>
Gene name
clpf-1
end case

Comments [?]

case <OC:Vertebrata>
Function Polynucleotide 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 RHEA:15669: a 5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP = a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + ADP + H(+)
EC 2.7.1.78
RHEA:54580: a 5'-end dephospho-ribonucleoside-RNA + ATP = a 5'-end 5'-monophospho-ribonucleoside-RNA + ADP + H(+)
EC 2.7.1.78
else case <OC:Saccharomyces>
Function Component 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.
else
Function Required for endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation.
end case
case <OC:Mammalia>
Cofactor Mg(2+)
Mn(2+)
Ni(2+)
end case
case <OC:Mammalia>
Subunit Component 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>
Subunit Component of the tRNA splicing endonuclease complex. Component of pre-mRNA cleavage complex II (CF-II).
else case <OC:Saccharomyces>
Subunit Component 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>
Subunit Component of a pre-mRNA cleavage factor complex. Interacts directly with PCF11.
end case
Subcellular location Nucleus.
Similarity Belongs to the Clp1 family. Clp1 subfamily.
case <OC:Fungi>
Caution May lack the polyribonucleotide 5'-hydroxyl-kinase and polynucleotide 5'-hydroxyl-kinase activities that are characteristic of the human ortholog.
end case

Keywords [?]

mRNA processing
Nucleus
case <FTTag:atp>
ATP-binding
Nucleotide-binding
end case
case <OC:Vertebrata>
Kinase
Transferase
tRNA processing
end case
case <OC:Mammalia>
Magnesium
Manganese
Nickel
end case

Gene Ontology [?]

GO:0005524; Molecular function: ATP binding.
GO:0031124; Biological process: mRNA 3'-end processing.
GO:0005634; Cellular component: nucleus.
case <OC: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 <OC:Vertebrata>
GO:0000214; Cellular component: tRNA-intron endonuclease complex.
end case
case <OC: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" /ligand_id="ChEBI:CHEBI:30616   atp   x-x-G-[KR]-[ST]-[STA]  
BINDING (Optional)     33     33       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     [DE]  
BINDING (Optional)     72     72       /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616     [KR]  

Additional information [?]

Size range 423-665 amino acids
Related rules None
Fusion None


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