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    Pnkp polynucleotide kinase 3'- phosphatase [ Mus musculus (house mouse) ]

    Gene ID: 59047, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Pnkpprovided by MGI
    Official Full Name
    polynucleotide kinase 3'- phosphataseprovided by MGI
    Primary source
    MGI:MGI:1891698
    See related
    Ensembl:ENSMUSG00000002963 AllianceGenome:MGI:1891698
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    PNK; 1810009G08Rik
    Summary
    Enables ubiquitin-like ligase-substrate adaptor activity. Involved in DNA damage response and protein K63-linked ubiquitination. Part of SCF ubiquitin ligase complex. Is active in site of double-strand break. Is expressed in cerebellum; cerebral cortex; liver; and spleen. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease type 2B2; ataxia-oculomotor apraxia type 4; and microcephaly, seizures, and developmental delay. Orthologous to human PNKP (polynucleotide kinase 3'-phosphatase). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in adrenal adult (RPKM 14.6), thymus adult (RPKM 14.2) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pnkp in Genome Data Viewer
    Location:
    7 B3; 7 28.94 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (44505903..44514761)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (44856479..44865337)

    Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene interleukin 4 induced 1B Neighboring gene interleukin 4 induced 1 Neighboring gene TBC1 domain family, member 17 Neighboring gene CapStarr-seq enhancer MGSCv37_chr7:52112565-52112765 Neighboring gene AKT1 substrate 1 Neighboring gene microRNA 707 Neighboring gene prostate tumor over expressed gene 1 Neighboring gene mediator complex subunit 25 Neighboring gene STARR-positive B cell enhancer ABC_E8171 Neighboring gene STARR-positive B cell enhancer ABC_E547 Neighboring gene fuzzy planar cell polarity protein Neighboring gene adaptor-related protein complex 2, alpha 1 subunit

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase. Bernstein NK, et al. Mol Cell, 2005 Mar 4. PMID 15749016
    2. Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase. Bernstein NK, et al. Nucleic Acids Res, 2009 Oct. PMID 19671525, Free PMC Article
    3. The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase. Garces F, et al. Mol Cell, 2011 Nov 4. PMID 22055185, Free PMC Article
    4. Characterization of DNA Substrate Binding to the Phosphatase Domain of the DNA Repair Enzyme Polynucleotide Kinase/Phosphatase. Havali-Shahriari Z, et al. Biochemistry, 2017 Mar 28. PMID 28276686, Free PMC Article
    5. Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates. Coquelle N, et al. Proc Natl Acad Sci U S A, 2011 Dec 27. PMID 22171004, Free PMC Article

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Fructose-2,6-bisphosphate restores DNA repair activity of PNKP and ameliorates neurodegenerative symptoms in Huntington's disease.
      Title: Fructose-2,6-bisphosphate restores DNA repair activity of PNKP and ameliorates neurodegenerative symptoms in Huntington's disease.
    2. PNKP is required for maintaining the integrity of progenitor cell populations in adult mice.
      Title: PNKP is required for maintaining the integrity of progenitor cell populations in adult mice.
    3. Repair independent of the well documented XRCC1-PNKP interaction was studied. XRCC1 can mediate repair of strand breaks without PNKP binding.
      Title: XRCC1-mediated repair of strand breaks independent of PNKP binding.
    4. The work indicates that the phosphatase domain of Pnkp binds 3'-phosphorylated single-stranded DNAs in a manner that is highly dependent on the presence of the 3'-phosphate.
      Title: Characterization of DNA Substrate Binding to the Phosphatase Domain of the DNA Repair Enzyme Polynucleotide Kinase/Phosphatase.
    5. Directed postnatal neural inactivation of PNKP affected specific subpopulations including oligodendrocytes, indicating a broad requirement for genome maintenance, both during and after neurogenesis.
      Title: Polynucleotide kinase-phosphatase enables neurogenesis via multiple DNA repair pathways to maintain genome stability.
    6. Structure of dsDNA bound to PNK 5'-kinase domain reveals DNA bending facilitating recognition of DNA ends in the context of single-strand/double-strand breaks, suggesting close functional cooperation in between the kinase/phosphatase active sites.
      Title: The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase.
    7. analysis of the molecular architecture of polynucleotide kinase
      Title: The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables polynucleotide 3'-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables polynucleotide 3'-phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables polynucleotide 3'-phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin-like ligase-substrate adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA ligation involved in DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA ligation involved in DNA repair ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of protein ADP-ribosylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in phosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of telomere capping ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of telomere maintenance via telomerase ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K63-linked ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to oxidative stress ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of SCF ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    bifunctional polynucleotide phosphatase/kinase
    Names
    DNA 5'-kinase/3'-phosphatase
    NP_001277693.1
    NP_001277695.1
    NP_001277696.1
    NP_067524.2
    XP_006541101.2
    XP_006541102.2
    XP_006541103.2
    XP_006541104.1
    XP_006541105.2
    XP_011249187.1
    XP_017177921.1
    XP_030098705.1
    XP_030098706.1
    XP_030098707.1
    XP_030098708.1
    XP_030098709.1
    XP_036009200.1
    XP_036009201.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001290764.1 → NP_001277693.1  bifunctional polynucleotide phosphatase/kinase isoform a

      See identical proteins and their annotated locations for NP_001277693.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC158231, AK049992, BY118349, BY579541
      Consensus CDS
      CCDS39945.1
      UniProtKB/Swiss-Prot
      Q6PFA3, Q9JLV6
      UniProtKB/TrEMBL
      G5E8N7
      Related
      ENSMUSP00000103508.2, ENSMUST00000107876.8
      Conserved Domains (3) summary
      cd01427
      Location:168 → 288
      HAD_like; Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, ...
      TIGR01663
      Location:3 → 522
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase
      cl17190
      Location:366 → 442
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    2. NM_001290766.1 → NP_001277695.1  bifunctional polynucleotide phosphatase/kinase isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AK049992, BC047269, BY118349, BY579541, CX223963
      Consensus CDS
      CCDS71955.1
      UniProtKB/TrEMBL
      E9Q9A5, Q3T9F5
      Related
      ENSMUSP00000096078.4, ENSMUST00000098478.7
      Conserved Domains (1) summary
      TIGR01663
      Location:3 → 486
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    3. NM_001290767.1 → NP_001277696.1  bifunctional polynucleotide phosphatase/kinase isoform c

      See identical proteins and their annotated locations for NP_001277696.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate exon and uses a downstream start codon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AK049992, BY579541, CK628081
      Conserved Domains (1) summary
      TIGR01663
      Location:1 → 304
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    4. NM_021549.3 → NP_067524.2  bifunctional polynucleotide phosphatase/kinase isoform a

      See identical proteins and their annotated locations for NP_067524.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC158231, AK049992, BY118349, BY579541, CX223963
      Consensus CDS
      CCDS39945.1
      UniProtKB/Swiss-Prot
      Q6PFA3, Q9JLV6
      UniProtKB/TrEMBL
      G5E8N7
      Related
      ENSMUSP00000003044.8, ENSMUST00000003044.14
      Conserved Domains (3) summary
      cd01427
      Location:168 → 288
      HAD_like; Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, ...
      TIGR01663
      Location:3 → 522
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase
      cl17190
      Location:366 → 442
      NK; Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates ...

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000073.7 Reference GRCm39 C57BL/6J

      Range
      44505903..44514761
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017322432.2 → XP_017177921.1  bifunctional polynucleotide phosphatase/kinase isoform X11

      Conserved Domains (1) summary
      TIGR01663
      Location:1 → 264
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    2. XM_030242848.1 → XP_030098708.1  bifunctional polynucleotide phosphatase/kinase isoform X12

      Conserved Domains (1) summary
      TIGR01663
      Location:1 → 219
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    3. XM_030242849.1 → XP_030098709.1  bifunctional polynucleotide phosphatase/kinase isoform X13

      Conserved Domains (1) summary
      TIGR01663
      Location:1 → 304
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    4. XM_006541039.5 → XP_006541102.2  bifunctional polynucleotide phosphatase/kinase isoform X2

      Conserved Domains (1) summary
      TIGR01663
      Location:17 → 474
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    5. XM_030242847.2 → XP_030098707.1  bifunctional polynucleotide phosphatase/kinase isoform X10

      UniProtKB/TrEMBL
      Q3T9F5
      Conserved Domains (1) summary
      TIGR01663
      Location:3 → 464
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    6. XM_030242846.2 → XP_030098706.1  bifunctional polynucleotide phosphatase/kinase isoform X7

      Conserved Domains (1) summary
      TIGR01663
      Location:3 → 446
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    7. XM_006541040.4 → XP_006541103.2  bifunctional polynucleotide phosphatase/kinase isoform X3

      Conserved Domains (1) summary
      TIGR01663
      Location:17 → 460
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    8. XM_006541041.5 → XP_006541104.1  bifunctional polynucleotide phosphatase/kinase isoform X4

      UniProtKB/Swiss-Prot
      Q6PFA3, Q9JLV6
      Conserved Domains (1) summary
      TIGR01663
      Location:3 → 482
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    9. XM_006541038.5 → XP_006541101.2  bifunctional polynucleotide phosphatase/kinase isoform X1

      Conserved Domains (1) summary
      TIGR01663
      Location:17 → 496
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    10. XM_030242845.2 → XP_030098705.1  bifunctional polynucleotide phosphatase/kinase isoform X6

      UniProtKB/Swiss-Prot
      Q6PFA3, Q9JLV6
      Conserved Domains (1) summary
      TIGR01663
      Location:17 → 514
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    11. XM_036153308.1 → XP_036009201.1  bifunctional polynucleotide phosphatase/kinase isoform X11

      Conserved Domains (1) summary
      TIGR01663
      Location:1 → 264
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    12. XM_036153307.1 → XP_036009200.1  bifunctional polynucleotide phosphatase/kinase isoform X9

      UniProtKB/TrEMBL
      E9Q9A5, Q3T9F5
      Conserved Domains (1) summary
      TIGR01663
      Location:3 → 486
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    13. XM_011250885.3 → XP_011249187.1  bifunctional polynucleotide phosphatase/kinase isoform X8

      UniProtKB/TrEMBL
      Q3T9F5
      Conserved Domains (1) summary
      TIGR01663
      Location:17 → 500
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    14. XM_006541042.4 → XP_006541105.2  bifunctional polynucleotide phosphatase/kinase isoform X5

      UniProtKB/Swiss-Prot
      Q6PFA3, Q9JLV6
      Conserved Domains (1) summary
      TIGR01663
      Location:17 → 536
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

    RNA

    1. XR_003946531.2 RNA Sequence

      Related
      ENSMUST00000155050.5
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9JLV6.2 GenPept UniProtKB/Swiss-Prot:Q9JLV6

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