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

Gene ID: 59047, updated on 2-Nov-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, Nov 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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