PNKP polynucleotide kinase 3'-phosphatase [Homo sapiens] - Gene

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Summary

Official Symbol: PNKPprovided by HGNC
Official Full Name: polynucleotide kinase 3'-phosphataseprovided by HGNC
Primary source: HGNC:9154
See related: Ensembl:ENSG00000039650; HPRD:09284; 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; 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]

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Genomic context

Location :: 19q13.3-q13.4

Sequence :: Chromosome: 19; NC_000019.9 (50364460..50370822, complement)

See PNKP in Epigenomics, MapViewer

Chromosome 19 - NC_000019.9 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

the critical role of NEIL2 and PNKP in maintenance of the mammalian mitochondrial genome.
Title: Role of human DNA glycosylase Nei-like 2 (NEIL2) and single strand break repair protein polynucleotide kinase 3'-phosphatase in maintenance of mitochondrial genome.
PNKP distorts target DNA structures to access damaged substrate DNA ends, thus providing a molecular mechanism for the involvement of PNKP in the repair of both single- and double-strand breaks.
Title: Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates.
Results reveal that ionizing radiation-induced phosphorylation of PNKP by ATM and DNA-PK regulates PNKP function at DNA double strand breaks.
Title: Phosphorylation of polynucleotide kinase/ phosphatase by DNA-dependent protein kinase and ataxia-telangiectasia mutated regulates its association with sites of DNA damage.
Studies indicate that PNKP serves a crucial role in the repair of DNA strand breaks through interactions with other DNA repair proteins, notably XRCC1 and XRCC4.
Title: Tidying up loose ends: the role of polynucleotide kinase/phosphatase in DNA strand break repair.
CK2-mediated phosphorylation of XRCC4 can have different effects on PNKP activity.
Title: Dual modes of interaction between XRCC4 and polynucleotide kinase/phosphatase: implications for nonhomologous end joining.
Observational study of gene-disease association. (HuGE Navigator)
Title: Polymorphisms in the base excision repair pathway and graft-versus-host disease.
The neurological abnormalities in individuals with microcephaly, early onset, intractable seizures and develomental delays may reflect a role for PNKP in several DNA repair pathways.
Title: Mutations in PNKP cause microcephaly, seizures and defects in DNA repair.
the FHA domain of PNK binds specifically, and with high affinity to a multiply phosphorylated motif in XRCC1 containing a pSer-pThr dipeptide, and forms a 2:1 PNK:XRCC1 complex.
Title: Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK.
The PNKP T5644G variant does not seem to be involved in adenoma recurrence in the Polyp Prevention Trial.
Title: Polynucleotide kinase 3' phosphatase variant, dietary variables and risk of adenoma recurrence in the Polyp Prevention Trial.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Polynucleotide kinase 3' phosphatase variant, dietary variables and risk of adenoma recurrence in the Polyp Prevention Trial.

Submit: New GeneRIF Correction See all (15)

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Phenotypes

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Epileptic encephalopathy, early infantile, 10

MIM: 613402

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Products	Interactant	Other Gene	Source	Pubs	Description
NP_009185.2	NP_006288.1	XRCC1	BIND	PubMed	Phosphorylated XRCC1 interacts with PNK.
NP_009185.2			BIND	PubMed	PNK removes 3' phosphate of DNA.
Q96T60	Q9BQ66	KRTAP4-12	HPRD	PubMed
Q96T60	P43364	MAGEA11	HPRD	PubMed
Q96T60	Q9NP98	MYOZ1	HPRD	PubMed
Q96T60	Q99717	SMAD5	HPRD	PubMed
Q96T60	O94972	TRIM37	HPRD	PubMed
Q96T60	P18887	XRCC1	HPRD	PubMed
Q96T60	Q13426	XRCC4	HPRD	PubMed
BioGRID:116440	BioGRID:123774	ATAD3B	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:116387	DDX20	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:120260	HEATR2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:123756	KRTAP4-12	BioGRID	PubMed	Two-hybrid
BioGRID:116440	BioGRID:123620	LAS1L	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:110168	LIG3	BioGRID	PubMed	Affinity Capture-MS; Affinity Capture-Western; Two-hybrid
BioGRID:116440	BioGRID:110169	LIG4	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:110284	MAGEA11	BioGRID	PubMed	Two-hybrid
BioGRID:116440	BioGRID:110340	MCM3	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:121849	MYOZ1	BioGRID	PubMed	Two-hybrid
BioGRID:116440	BioGRID:114477	NOL3	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:122182	NOM1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:115041	NUP93	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:111419	POLB	BioGRID	PubMed	Affinity Capture-Western; Two-hybrid
BioGRID:116440	BioGRID:114164	SLC25A12	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:110678	TRIM37	BioGRID	PubMed	Two-hybrid
BioGRID:116440	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:113349	XRCC1	BioGRID	PubMed	Affinity Capture-MS; Affinity Capture-Western; Far Western; Two-hybrid
BioGRID:116440	BioGRID:113352	XRCC4	BioGRID	PubMed	Affinity Capture-MS
BioGRID:116440	BioGRID:116168	YWHAQ	BioGRID	PubMed	Affinity Capture-MS

Function	Evidence Code	Pubs
ATP binding	NAS Non-traceable Author Statement 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	TAS Traceable Author Statement more info	PubMed
endonuclease activity	NAS Non-traceable Author Statement more info	PubMed
hydrolase activity	IEA Inferred from Electronic Annotation more info
kinase activity	IEA Inferred from Electronic Annotation more info
nucleotide kinase activity	IDA Inferred from Direct Assay more info	PubMed
polynucleotide 3'-phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
purine nucleotide binding	NAS Non-traceable Author Statement more info	PubMed
transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
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	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
nucleotide phosphorylation	IDA Inferred from Direct Assay more info	PubMed
nucleotide-excision repair, DNA damage removal	NAS Non-traceable Author Statement 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
nucleolus	IDA Inferred from Direct Assay more info	PubMed
NOT nucleolus	IDA Inferred from Direct Assay more info	PubMed
nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

Preferred Names: bifunctional polynucleotide phosphatase/kinase

Names: bifunctional polynucleotide phosphatase/kinase; DNA 5'-kinase/3'-phosphatase; Homo sapiens polynucleotide kinase 3'-phosphatase (PNKP)

NP_009185.2

EC 2.7.1.78

EC 3.1.3.32

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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

NG_027717.1 RefSeqGene

Range

5001..11363

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_007254.3 → NP_009185.2 bifunctional polynucleotide phosphatase/kinase

Status: REVIEWED

Source sequence(s)

AA640353, BC033822, BU541073

Consensus CDS

CCDS12783.1

UniProtKB/Swiss-Prot

Q96T60

Related

ENSP00000323511, ENST00000322344

Conserved Domains (2) summary

cd01427
Location:170 – 289
Blast Score: 121

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:2 – 521
Blast Score: 2376

PNK-3'Pase; polynucleotide 5'-kinase 3'-phosphatase

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000019.9 Reference GRCh37.p5 Primary Assembly

Range

50364460..50370822, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000151.1 Alternate HuRef

Range

46740801..46747159, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AC018766.2	AAF44716.1
genomic	AC118341.2 (1812..3252)	None
genomic	AF354258.1	AAK57340.1
genomic	AY133033.1	AAM82170.1
genomic	CH471177.1	EAW52565.1
		EAW52566.1
		EAW52567.1
mRNA	AA640353.1	None
mRNA	AF120499.1	AAD47379.1
mRNA	AF125807.1	AAD50639.1
mRNA	AF126486.1	AAD51135.1
mRNA	BC002519.2	AAH02519.2
mRNA	BC009339.2	None
mRNA	BC013034.2	None
mRNA	BC033822.1	AAH33822.1
mRNA	BU541073.1	None
other-genetic	DQ890806.2	ABM81732.1
other-genetic	DQ893961.2	ABM84887.1