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Protein

Polyribonucleotide 5'-hydroxyl-kinase Clp1

Gene

Clp1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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 Publications

Catalytic activityi

ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.UniRule annotation
ATP + 5'-dephospho-RNA = ADP + 5'-phospho-RNA.UniRule annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation, Ni2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei22 – 221ATPUniRule annotation
Binding sitei62 – 621ATP; via carbonyl oxygenUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi124 – 1296ATPUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

mRNA processing, tRNA processing

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Nickel, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-MMU-109688. Cleavage of Growing Transcript in the Termination Region.
R-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72187. mRNA 3'-end processing.
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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:2138968. Clp1.

Subcellular locationi

  • Nucleus UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Early embryonic lethality.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi127 – 1271K → 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

Keywords - Diseasei

Neurodegeneration

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 425425Polyribonucleotide 5'-hydroxyl-kinase Clp1PRO_0000089864Add
BLAST

Proteomic databases

EPDiQ99LI9.
MaxQBiQ99LI9.
PaxDbiQ99LI9.
PeptideAtlasiQ99LI9.
PRIDEiQ99LI9.

PTM databases

iPTMnetiQ99LI9.
PhosphoSiteiQ99LI9.

Expressioni

Gene expression databases

BgeeiENSMUSG00000027079.
GenevisibleiQ99LI9. 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 annotation

Protein-protein interaction databases

BioGridi221164. 9 interactions.
IntActiQ99LI9. 9 interactions.
STRINGi10090.ENSMUSP00000028475.

Structurei

3D structure databases

ProteinModelPortaliQ99LI9.
SMRiQ99LI9. Positions 14-423.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the Clp1 family. Clp1 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiKOG2749. Eukaryota.
COG5623. LUCA.
GeneTreeiENSGT00390000000344.
HOGENOMiHOG000231935.
HOVERGENiHBG000921.
InParanoidiQ99LI9.
KOiK14399.
OMAiAGFCCVT.
OrthoDBiEOG091G088L.
PhylomeDBiQ99LI9.
TreeFamiTF105795.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_03035. Clp1. 1 hit.
InterProiIPR028606. Clp1.
IPR032324. Clp1_N.
IPR032319. CLP1_P.
IPR027417. P-loop_NTPase.
IPR010655. Pre-mRNA_cleavage_Clp1.
[Graphical view]
PfamiPF06807. Clp1. 1 hit.
PF16573. CLP1_N. 1 hit.
PF16575. CLP1_P. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.

Sequencei

Sequence statusi: Complete.

Q99LI9-1 [UniParc]FASTAAdd to basket

« Hide

        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
Length:425
Mass (Da):47,738
Last modified:June 1, 2001 - v1
Checksum:iC1AED7978B383097
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti79 – 791T → N in BAE26299 (PubMed:16141072).Curated
Sequence conflicti264 – 2641N → D in BAE41321 (PubMed:16141072).Curated
Sequence conflicti394 – 3941V → L in BAE26299 (PubMed:16141072).Curated

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.
CCDSiCCDS16191.1.
RefSeqiNP_598601.1. NM_133840.2.
UniGeneiMm.21583.

Genome annotation databases

EnsembliENSMUST00000028475; ENSMUSP00000028475; ENSMUSG00000027079.
ENSMUST00000165219; ENSMUSP00000129300; ENSMUSG00000027079.
GeneIDi98985.
KEGGimmu:98985.
UCSCiuc008kja.1. mouse.

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.
CCDSiCCDS16191.1.
RefSeqiNP_598601.1. NM_133840.2.
UniGeneiMm.21583.

3D structure databases

ProteinModelPortaliQ99LI9.
SMRiQ99LI9. Positions 14-423.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi221164. 9 interactions.
IntActiQ99LI9. 9 interactions.
STRINGi10090.ENSMUSP00000028475.

PTM databases

iPTMnetiQ99LI9.
PhosphoSiteiQ99LI9.

Proteomic databases

EPDiQ99LI9.
MaxQBiQ99LI9.
PaxDbiQ99LI9.
PeptideAtlasiQ99LI9.
PRIDEiQ99LI9.

Protocols and materials databases

DNASUi98985.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000028475; ENSMUSP00000028475; ENSMUSG00000027079.
ENSMUST00000165219; ENSMUSP00000129300; ENSMUSG00000027079.
GeneIDi98985.
KEGGimmu:98985.
UCSCiuc008kja.1. mouse.

Organism-specific databases

CTDi10978.
MGIiMGI:2138968. Clp1.

Phylogenomic databases

eggNOGiKOG2749. Eukaryota.
COG5623. LUCA.
GeneTreeiENSGT00390000000344.
HOGENOMiHOG000231935.
HOVERGENiHBG000921.
InParanoidiQ99LI9.
KOiK14399.
OMAiAGFCCVT.
OrthoDBiEOG091G088L.
PhylomeDBiQ99LI9.
TreeFamiTF105795.

Enzyme and pathway databases

ReactomeiR-MMU-109688. Cleavage of Growing Transcript in the Termination Region.
R-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72187. mRNA 3'-end processing.
R-MMU-77595. Processing of Intronless Pre-mRNAs.

Miscellaneous databases

PROiQ99LI9.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000027079.
GenevisibleiQ99LI9. MM.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_03035. Clp1. 1 hit.
InterProiIPR028606. Clp1.
IPR032324. Clp1_N.
IPR032319. CLP1_P.
IPR027417. P-loop_NTPase.
IPR010655. Pre-mRNA_cleavage_Clp1.
[Graphical view]
PfamiPF06807. Clp1. 1 hit.
PF16573. CLP1_N. 1 hit.
PF16575. CLP1_P. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
ProtoNetiSearch...

Entry informationi

Entry nameiCLP1_MOUSE
AccessioniPrimary (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: September 7, 2016
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.