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

Summary

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 ligase-substrate adaptor activity. Involved in cellular response to DNA damage stimulus 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 and microcephaly, seizures, and developmental delay. Orthologous to human PNKP (polynucleotide kinase 3'-phosphatase). [provided by Alliance of Genome Resources, Apr 2022]
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

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_000073.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
analysis of the molecular architecture of polynucleotide kinase
Title: The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.

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Variation

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Alleles

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

Endonuclease-mediated (2) 1 citation
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH125290 (e-PCR)
- UniSTS:162112

AU041779 (e-PCR)
- UniSTS:159635

RH124360 (e-PCR)
- UniSTS:161182

RH128074 (e-PCR)
- UniSTS:211382

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	ISO Inferred from Sequence Orthology more info
enables ATP-dependent polynucleotide 5'-hydroxyl-kinase activity	IEA Inferred from Electronic Annotation more info
enables catalytic activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables kinase activity	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables polynucleotide 3'-phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables polynucleotide 3'-phosphatase activity	ISO Inferred from Sequence Orthology more info
enables transferase activity	IEA Inferred from Electronic Annotation 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 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
acts_upstream_of_or_within metabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein ADP-ribosylation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within 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 telomerase activity	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	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

EC 2.7.1.78

EC 3.1.3.32

NP_001277695.1

EC 2.7.1.78

EC 3.1.3.32

NP_001277696.1

EC 2.7.1.78

EC 3.1.3.32

NP_067524.2

EC 2.7.1.78

EC 3.1.3.32

XP_006541101.2

EC 2.7.1.78

EC 3.1.3.32

XP_006541102.2

EC 2.7.1.78

EC 3.1.3.32

XP_006541103.2

EC 2.7.1.78

EC 3.1.3.32

XP_006541104.1

EC 2.7.1.78

EC 3.1.3.32

XP_006541105.2

EC 2.7.1.78

EC 3.1.3.32

XP_011249187.1

EC 2.7.1.78

EC 3.1.3.32

XP_017177921.1

EC 2.7.1.78

EC 3.1.3.32

XP_030098705.1

EC 2.7.1.78

EC 3.1.3.32

XP_030098706.1

EC 2.7.1.78

EC 3.1.3.32

XP_030098707.1

EC 2.7.1.78

EC 3.1.3.32

XP_030098708.1

EC 2.7.1.78

EC 3.1.3.32

XP_030098709.1

EC 2.7.1.78

EC 3.1.3.32

XP_036009200.1

EC 2.7.1.78

EC 3.1.3.32

XP_036009201.1

EC 2.7.1.78

EC 3.1.3.32

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)

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 ...
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
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
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

NC_000073.7 Reference GRCm39 C57BL/6J

Range

44505903..44514761

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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
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
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
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
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
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
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