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    PNKP polynucleotide kinase 3'-phosphatase [ Homo sapiens (human) ]

    Gene ID: 11284, updated on 23-Nov-2023

    Summary

    Official Symbol
    PNKPprovided by HGNC
    Official Full Name
    polynucleotide kinase 3'-phosphataseprovided by HGNC
    Primary source
    HGNC:HGNC:9154
    See related
    Ensembl:ENSG00000039650 MIM:605610; AllianceGenome:HGNC:9154
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PNK; AOA4; MCSZ; CMT2B2; EIEE10
    Summary
    This locus represents a gene involved in DNA repair. In response to ionizing radiation or oxidative damage, the protein encoded by this locus catalyzes 5' phosphorylation and 3' dephosphorylation of nucleic acids. Mutations at this locus have been associated with microcephaly, seizures, and developmental delay.[provided by RefSeq, Sep 2010]
    Expression
    Ubiquitous expression in spleen (RPKM 18.2), adrenal (RPKM 13.4) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PNKP in Genome Data Viewer
    Location:
    19q13.33
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (49861204..49867576, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (52861341..52867713, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50364461..50370833, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene PTOV1 extended AT-hook containing adaptor protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14963 Neighboring gene microRNA 4749 Neighboring gene PTOV1 antisense RNA 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50368723-50369505 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50369506-50370288 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50370289-50371070 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50373269-50373916 Neighboring gene AKT1 substrate 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50379233-50380192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14965 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50381153-50382112 Neighboring gene TBC1 domain family member 17 Neighboring gene uncharacterized LOC124904743 Neighboring gene microRNA 4750

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, polynucleotide kinase 3'-phosphatase (PNKP), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: AKT1S1

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables damaged DNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables double-stranded DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables endonuclease activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables polynucleotide 3'-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables polynucleotide 3'-phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables polynucleotide 3'-phosphatase activity TAS
    Traceable Author Statement
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables purine nucleotide binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA ligation involved in DNA repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in DNA repair IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in DNA-templated DNA replication NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in base-excision repair, gap-filling TAS
    Traceable Author Statement
    more info
     
    involved_in double-strand break repair via nonhomologous end joining IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of protein ADP-ribosylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nucleotide-excision repair TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in phosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of double-strand break repair via nonhomologous end joining IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of telomerase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of telomere capping IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of telomere maintenance via telomerase IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to oxidative stress IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to radiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in response to radiation TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in membrane HDA PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    bifunctional polynucleotide phosphatase/kinase
    Names
    DNA 5'-kinase/3'-phosphatase
    Homo sapiens polynucleotide kinase 3'-phosphatase (PNKP)
    NP_009185.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_027717.1 RefSeqGene

      Range
      4990..11362
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_007254.4NP_009185.2  bifunctional polynucleotide phosphatase/kinase

      See identical proteins and their annotated locations for NP_009185.2

      Status: REVIEWED

      Source sequence(s)
      AC118341, BC033822, BU541073
      Consensus CDS
      CCDS12783.1
      UniProtKB/Swiss-Prot
      Q96T60, Q9BUL2, Q9P1V2, Q9UKU8, Q9UNF8, Q9UNI0
      UniProtKB/TrEMBL
      A0A1S5RA93
      Related
      ENSP00000323511.2, ENST00000322344.8
      Conserved Domains (3) summary
      cd01427
      Location:170289
      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:2521
      PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase
      cl17190
      Location:367465
      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_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      49861204..49867576 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      52861341..52867713 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)