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

Gene ID: 11284, updated on 9-Dec-2018

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
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; 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

Genomic context

See PNKP in Genome Data Viewer
Location:
19q13.33
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (49861203..49867565, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50364460..50370840, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene PTOV1, extended AT-hook containing adaptor protein Neighboring gene microRNA 4749 Neighboring gene PTOV1 antisense RNA 2 Neighboring gene AKT1 substrate 1 Neighboring gene TBC1 domain family member 17 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 FunctionsWhat'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 BioSystems

  • APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway, organism-specific biosystem (from REACTOME)
    APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway, organism-specific biosystemNEIL1 and NEIL2 have a dual DNA glycosylase and beta/delta lyase activity. The AP (apurinic/apyrimidinic) site-directed lyase activity of NEIL1 and NEIL2 is their major physiological role, as they ca...
  • Base Excision Repair, organism-specific biosystem (from REACTOME)
    Base Excision Repair, organism-specific biosystemOf the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of ...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Resolution of Abasic Sites (AP sites), organism-specific biosystem (from REACTOME)
    Resolution of Abasic Sites (AP sites), organism-specific biosystemResolution of AP sites can occur through the single nucleotide replacement pathway or through the multiple nucleotide patch replacement pathway, also known as the long-patch base excision repair (BER...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: AKT1S1

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding NAS
Non-traceable Author Statement
more info
PubMed 
ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
damaged DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-stranded DNA binding TAS
Traceable Author Statement
more info
PubMed 
endonuclease activity NAS
Non-traceable Author Statement
more info
PubMed 
nucleoside monophosphate kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoside monophosphate kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
polynucleotide 3'-phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
polynucleotide 3'-phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
polynucleotide 3'-phosphatase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
purine nucleotide binding NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
DNA 3' dephosphorylation involved in DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA damage response, detection of DNA damage IDA
Inferred from Direct Assay
more info
PubMed 
DNA damage response, detection of DNA damage NAS
Non-traceable Author Statement
more info
PubMed 
DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA repair IGI
Inferred from Genetic Interaction
more info
PubMed 
DNA-dependent DNA replication NAS
Non-traceable Author Statement
more info
PubMed 
dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of protein ADP-ribosylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 
nucleoside monophosphate phosphorylation IEA
Inferred from Electronic Annotation
more info
 
nucleotide phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleotide phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
nucleotide-excision repair, DNA damage removal NAS
Non-traceable Author Statement
more info
PubMed 
polynucleotide 3' dephosphorylation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of telomerase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of telomere capping IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of telomere maintenance via telomerase IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to oxidative stress IDA
Inferred from Direct Assay
more info
PubMed 
response to radiation NAS
Non-traceable Author Statement
more info
PubMed 
response to radiation TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
membrane HDA PubMed 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus 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)

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
    5001..11363
    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
    Related
    ENSP00000323511.2, ENST00000322344.7
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    49861203..49867565 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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