UniProtKB - Q99LI9 (CLP1_MOUSE)
Polyribonucleotide 5'-hydroxyl-kinase Clp1
Clp1
Functioni
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. Plays a key role 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 (PubMed:23474986, PubMed:24766809).
Its role in tRNA splicing and maturation is required for cerebellar development (PubMed:24766809).
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 DICER1 already contain a 5'-phosphate group, so this protein may be dispensible for normal RNA-mediated gene silencing.
2 PublicationsCatalytic activityi
- a 5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP = a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + ADP + H+UniRule annotationEC:2.7.1.78UniRule annotation
- a 5'-end dephospho-ribonucleoside-RNA + ATP = a 5'-end 5'-monophospho-ribonucleoside-RNA + ADP + H+UniRule annotationEC:2.7.1.78UniRule annotation
Cofactori
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 22 | ATPUniRule annotation | 1 | |
Binding sitei | 62 | ATP; via carbonyl oxygenUniRule annotation | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 124 – 129 | ATPUniRule annotation | 6 |
GO - Molecular functioni
- ATP binding Source: UniProtKB-UniRule
- polydeoxyribonucleotide 5'-hydroxyl-kinase activity Source: UniProtKB-EC
- polydeoxyribonucleotide kinase activity Source: UniProtKB
- polynucleotide 5'-hydroxyl-kinase activity Source: GO_Central
- polyribonucleotide 5'-hydroxyl-kinase activity Source: UniProtKB
GO - Biological processi
- cerebellar cortex development Source: UniProtKB
- mRNA polyadenylation Source: GO_Central
- RNA processing Source: GO_Central
- siRNA loading onto RISC involved in RNA interference Source: UniProtKB
- targeting of mRNA for destruction involved in RNA interference Source: UniProtKB
- tRNA splicing, via endonucleolytic cleavage and ligation Source: UniProtKB
Keywordsi
Molecular function | Kinase, Transferase |
Biological process | mRNA processing, tRNA processing |
Ligand | ATP-binding, Magnesium, Manganese, Nickel, Nucleotide-binding |
Enzyme and pathway databases
Reactomei | R-MMU-72163, mRNA Splicing - Major Pathway R-MMU-72187, mRNA 3'-end processing R-MMU-73856, RNA Polymerase II Transcription Termination R-MMU-77595, Processing of Intronless Pre-mRNAs |
Names & Taxonomyi
Protein namesi | Recommended name: Polyribonucleotide 5'-hydroxyl-kinase Clp1UniRule annotation (EC:2.7.1.78UniRule annotation)Alternative name(s): Polyadenylation factor Clp1UniRule annotation Polynucleotide kinase Clp1UniRule annotation Pre-mRNA cleavage complex II protein Clp1UniRule annotation |
Gene namesi | Name:Clp1 |
Organismi | Mus musculus (Mouse) |
Taxonomic identifieri | 10090 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus |
Proteomesi |
|
Organism-specific databases
MGIi | MGI:2138968, Clp1 |
VEuPathDBi | HostDB:ENSMUSG00000027079 |
Subcellular locationi
Nucleus
- Nucleus UniRule annotation
Cytosol
- cytosol Source: MGI
Nucleus
- mRNA cleavage factor complex Source: UniProtKB-UniRule
- nucleoplasm Source: MGI
- nucleus Source: MGI
- tRNA-intron endonuclease complex Source: UniProtKB
Keywords - Cellular componenti
NucleusPathology & Biotechi
Disruption phenotypei
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 127 | K → A: Progressive loss of motor neurons, axonal motor neuropathy, and muscle paralysis leading to death within hours of birth. Mice exhibit microcephaly due to reduced numbers of cortical neurons. Embryos have normal numbers and proliferation of neuronal progenitors, but neuronal progenitor cells undergo enhanced cell death, resulting in reduced numbers of cortical neurons. 2 Publications | 1 |
Keywords - Diseasei
NeurodegenerationPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000089864 | 1 – 425 | Polyribonucleotide 5'-hydroxyl-kinase Clp1Add BLAST | 425 |
Proteomic databases
EPDi | Q99LI9 |
MaxQBi | Q99LI9 |
PaxDbi | Q99LI9 |
PeptideAtlasi | Q99LI9 |
PRIDEi | Q99LI9 |
ProteomicsDBi | 283860 |
PTM databases
iPTMneti | Q99LI9 |
PhosphoSitePlusi | Q99LI9 |
Expressioni
Gene expression databases
Bgeei | ENSMUSG00000027079, Expressed in bone marrow and 306 other tissues |
Genevisiblei | Q99LI9, MM |
Interactioni
Subunit structurei
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.
UniRule annotationProtein-protein interaction databases
BioGRIDi | 221164, 9 interactors |
IntActi | Q99LI9, 9 interactors |
STRINGi | 10090.ENSMUSP00000028475 |
Miscellaneous databases
RNActi | Q99LI9, protein |
Family & Domainsi
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG2749, Eukaryota |
GeneTreei | ENSGT00940000153668 |
HOGENOMi | CLU_018195_1_0_1 |
InParanoidi | Q99LI9 |
OMAi | VQYVNCH |
OrthoDBi | 814241at2759 |
PhylomeDBi | Q99LI9 |
TreeFami | TF105795 |
Family and domain databases
Gene3Di | 2.40.30.330, 1 hit 2.60.120.1030, 1 hit 3.40.50.300, 1 hit |
HAMAPi | MF_03035, Clp1, 1 hit |
InterProi | View protein in InterPro IPR028606, Clp1 IPR045116, Clp1/Grc3 IPR010655, Clp1_C IPR038238, Clp1_C_sf IPR032324, Clp1_N IPR038239, Clp1_N_sf IPR032319, CLP1_P IPR027417, P-loop_NTPase |
PANTHERi | PTHR12755, PTHR12755, 1 hit |
Pfami | View protein in Pfam PF06807, Clp1, 1 hit PF16573, CLP1_N, 1 hit PF16575, CLP1_P, 1 hit |
SUPFAMi | SSF52540, SSF52540, 1 hit |
i Sequence
Sequence statusi: Complete.
10 20 30 40 50
MSEESNDDKK PTTKFELERE TELRFEVEAS QSVQLELLAG MAEIFGTELT
60 70 80 90 100
RNKKFTFDAG AKVAVFTWHG CSLQLSGRTE VAYVSKDTPM LLYLNTHTAL
110 120 130 140 150
EQMRRQAEKE EERGPRVMVV GPTDVGKSTV CRLLLNYAVR LGRRPTYVEL
160 170 180 190 200
DVGQGSVSIP GTMGALYIER PADVEEGFSI QAPLVYHFGS TTPGTNIKLY
210 220 230 240 250
NKITSRLADV FNQRCEVNRR ASVSGCVINT CGWVKGYGYQ ALVHAASAFE
260 270 280 290 300
VDVVVVLDQE RLYNELKRDL PHFVRTVLLP KSGGVVERSK DFRRECRDER
310 320 330 340 350
IREYFYGFRG CFYPHAFNVK FSDVKIYKVG APTIPDSCLP LGMSQEDNQL
360 370 380 390 400
KLVPVTPGRD MVHHLLSVST AEGTEENLSE TSVAGFIVVT SVDVEHQVFT
410 420
VLSPAPRPLP KNFLLIMDIR FMDLK
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 79 | T → N in BAE26299 (PubMed:16141072).Curated | 1 | |
Sequence conflicti | 264 | N → D in BAE41321 (PubMed:16141072).Curated | 1 | |
Sequence conflicti | 394 | V → L in BAE26299 (PubMed:16141072).Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AK077647 mRNA Translation: BAC36924.1 AK145209 mRNA Translation: BAE26299.1 AK169709 mRNA Translation: BAE41321.1 BC003237 mRNA Translation: AAH03237.1 |
CCDSi | CCDS16191.1 |
RefSeqi | NP_598601.1, NM_133840.2 |
Genome annotation databases
Ensembli | ENSMUST00000028475; ENSMUSP00000028475; ENSMUSG00000027079 ENSMUST00000165219; ENSMUSP00000129300; ENSMUSG00000027079 |
GeneIDi | 98985 |
KEGGi | mmu:98985 |
UCSCi | uc008kja.1, mouse |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AK077647 mRNA Translation: BAC36924.1 AK145209 mRNA Translation: BAE26299.1 AK169709 mRNA Translation: BAE41321.1 BC003237 mRNA Translation: AAH03237.1 |
CCDSi | CCDS16191.1 |
RefSeqi | NP_598601.1, NM_133840.2 |
3D structure databases
AlphaFoldDBi | Q99LI9 |
SMRi | Q99LI9 |
ModBasei | Search... |
Protein-protein interaction databases
BioGRIDi | 221164, 9 interactors |
IntActi | Q99LI9, 9 interactors |
STRINGi | 10090.ENSMUSP00000028475 |
PTM databases
iPTMneti | Q99LI9 |
PhosphoSitePlusi | Q99LI9 |
Proteomic databases
EPDi | Q99LI9 |
MaxQBi | Q99LI9 |
PaxDbi | Q99LI9 |
PeptideAtlasi | Q99LI9 |
PRIDEi | Q99LI9 |
ProteomicsDBi | 283860 |
Protocols and materials databases
Antibodypediai | 27467, 194 antibodies from 28 providers |
DNASUi | 98985 |
Genome annotation databases
Ensembli | ENSMUST00000028475; ENSMUSP00000028475; ENSMUSG00000027079 ENSMUST00000165219; ENSMUSP00000129300; ENSMUSG00000027079 |
GeneIDi | 98985 |
KEGGi | mmu:98985 |
UCSCi | uc008kja.1, mouse |
Organism-specific databases
CTDi | 10978 |
MGIi | MGI:2138968, Clp1 |
VEuPathDBi | HostDB:ENSMUSG00000027079 |
Phylogenomic databases
eggNOGi | KOG2749, Eukaryota |
GeneTreei | ENSGT00940000153668 |
HOGENOMi | CLU_018195_1_0_1 |
InParanoidi | Q99LI9 |
OMAi | VQYVNCH |
OrthoDBi | 814241at2759 |
PhylomeDBi | Q99LI9 |
TreeFami | TF105795 |
Enzyme and pathway databases
Reactomei | R-MMU-72163, mRNA Splicing - Major Pathway R-MMU-72187, mRNA 3'-end processing R-MMU-73856, RNA Polymerase II Transcription Termination R-MMU-77595, Processing of Intronless Pre-mRNAs |
Miscellaneous databases
BioGRID-ORCSi | 98985, 30 hits in 72 CRISPR screens |
PROi | PR:Q99LI9 |
RNActi | Q99LI9, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSMUSG00000027079, Expressed in bone marrow and 306 other tissues |
Genevisiblei | Q99LI9, MM |
Family and domain databases
Gene3Di | 2.40.30.330, 1 hit 2.60.120.1030, 1 hit 3.40.50.300, 1 hit |
HAMAPi | MF_03035, Clp1, 1 hit |
InterProi | View protein in InterPro IPR028606, Clp1 IPR045116, Clp1/Grc3 IPR010655, Clp1_C IPR038238, Clp1_C_sf IPR032324, Clp1_N IPR038239, Clp1_N_sf IPR032319, CLP1_P IPR027417, P-loop_NTPase |
PANTHERi | PTHR12755, PTHR12755, 1 hit |
Pfami | View protein in Pfam PF06807, Clp1, 1 hit PF16573, CLP1_N, 1 hit PF16575, CLP1_P, 1 hit |
SUPFAMi | SSF52540, SSF52540, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | CLP1_MOUSE | |
Accessioni | Q99LI9Primary (citable) accession number: Q99LI9 Secondary accession number(s): Q3TEC7, Q3ULZ9 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | January 4, 2005 |
Last sequence update: | June 1, 2001 | |
Last modified: | May 25, 2022 | |
This is version 126 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- MGD cross-references
Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot - SIMILARITY comments
Index of protein domains and families