HAMAP rule MF_03035
General rule information
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| PURL | https://purl.expasy.org/hamap/rule/MF_03035 |
| 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
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Identifier, protein and gene names
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| 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 | Name=CLP1; |
| else case <OC:Caenorhabditis> | |
| Gene name | Name=clpf-1; |
| end case | |
Comments
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| 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 | 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=2.7.1.78; |
| 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=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 | 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> | |
| 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
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| 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
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| 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
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| Pfam | PF06807; Clp1; 1; |
Features
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| 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 | 33 | 33 | /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616" |
[DE] | ||||||||
| BINDING | 72 | 72 | /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616" |
[KR] | ||||||||
Additional information
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| Size range | 423-665 amino acids |
| Related rules |
None |
| Fusion | Nter: None Cter: None |