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Q9JLV6 (PNKP_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Bifunctional polynucleotide phosphatase/kinase
Alternative name(s):
DNA 5'-kinase/3'-phosphatase
Polynucleotide kinase-3'-phosphatase

Including the following 2 domains:

  1. Polynucleotide 3'-phosphatase
    EC=3.1.3.32
    Alternative name(s):
    2'(3')-polynucleotidase
  2. Polynucleotide 5'-hydroxyl-kinase
    EC=2.7.1.78
Gene names
Name:Pnkp
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length522 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone.

Catalytic activity

A 3'-phosphopolynucleotide + H2O = a polynucleotide + phosphate.

ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.

Subunit structure

Monomer. Ref.5

Subcellular location

Nucleus By similarity.

Domain

The FHA domain binds threonine-phosphorylated peptides from XRCC1/4, and is responsible for the recruitment of PNKP to the sites of DNA repair. The affinity is ten times greater if peptides are also phosphorylated on the serine preceeding the phosphothreonine. Ref.5

Sequence similarities

In the N-terminal section; belongs to the DNA 3' phosphatase family.

Contains 1 FHA domain.

Ontologies

Keywords
   Biological processDNA damage
DNA repair
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   LigandATP-binding
Nucleotide-binding
   Molecular functionHydrolase
Kinase
Transferase
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Multifunctional enzyme
Reference proteome
Gene Ontology (GO)
   Biological_processDNA repair

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity

Inferred from electronic annotation. Source: UniProtKB-EC

polynucleotide 3'-phosphatase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9JLV6-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q9JLV6-2)

The sequence of this isoform differs from the canonical sequence as follows:
     163-191: QGKVAAFDLDGTLITTRSGKVFPTSPSDW → RA
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 522522Bifunctional polynucleotide phosphatase/kinase
PRO_0000058479

Regions

Domain6 – 110105FHA
Nucleotide binding371 – 3788ATP Potential
Region145 – 336192Phosphatase
Region340 – 517178Kinase

Amino acid modifications

Modified residue11N-acetylmethionine By similarity
Modified residue1141Phosphoserine By similarity
Modified residue1221Phosphothreonine Ref.3

Natural variations

Alternative sequence163 – 19129QGKVA…SPSDW → RA in isoform 2.
VSP_010771

Experimental info

Mutagenesis441R → A: Abrogates phosphopeptide recognition. Ref.5
Mutagenesis451K → N: No effect on phosphopeptide recognition. Ref.5
Mutagenesis481R → A: Abrogates phosphopeptide recognition. Ref.5
Sequence conflict771H → Q in AAF36487. Ref.1
Sequence conflict2161Missing in AAF36487. Ref.1

Secondary structure

.................................................................................................. 522
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 19, 2004. Version 2.
Checksum: C691C0A6DA9F47FE

FASTA52257,223
        10         20         30         40         50         60 
MSQLGSRGRL WLQSPTGGPP PIFLPSDGQA LVLGRGPLTQ VTDRKCSRNQ VELIADPESR 

        70         80         90        100        110        120 
TVAVKQLGVN PSTVGVHELK PGLSGSLSLG DVLYLVNGLY PLTLRWEELS TSGSQPDAPP 

       130        140        150        160        170        180 
DTPGDPEEGE DTEPQKKRVR KSSLGWESLK KLLVFTASGV KPQGKVAAFD LDGTLITTRS 

       190        200        210        220        230        240 
GKVFPTSPSD WRILYPEIPK KLQELAAEGY KLVIFTNQMG IGRGKLPAEV FKGKVEAVLE 

       250        260        270        280        290        300 
KLGVPFQVLV ATHAGLNRKP VSGMWDHLQE QANEGIPISV EDSVFVGDAA GRLANWAPGR 

       310        320        330        340        350        360 
KKKDFSCADR LFALNVGLPF ATPEEFFLKW PAARFELPAF DPRTISSAGP LYLPESSSLL 

       370        380        390        400        410        420 
SPNPEVVVAV GFPGAGKSTF IQEHLVSAGY VHVNRDTLGS WQRCVSSCQA ALRQGKRVVI 

       430        440        450        460        470        480 
DNTNPDVPSR ARYIQCAKDA GVPCRCFNFC ATIEQARHNN RFREMTDPSH APVSDMVMFS 

       490        500        510        520 
YRKQFEPPTL AEGFLEILEI PFRLQEHLDP ALQRLYRQFS EG 

« Hide

Isoform 2 [UniParc].

Checksum: 6FE381B1531C953C
Show »

FASTA49554,373

References

« Hide 'large scale' references
[1]Beaulieu N., Lasko D.D.
Submitted (FEB-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
Strain: C57BL/6J.
Tissue: Spleen.
[2]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Strain: C57BL/6J.
Tissue: Mammary tumor.
[3]"ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage."
Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J.
Science 316:1160-1166(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-122, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Embryonic fibroblast.
[4]"The forkhead-associated (FHA) domain-like structure from mouse polynucleotide kinase 3'-phosphatase."
RIKEN structural genomics initiative (RSGI)
Submitted (FEB-2004) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 1-106.
[5]"The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase."
Bernstein N.K., Williams R.S., Rakovszky M.L., Cui D., Green R., Karimi-Busheri F., Mani R.S., Galicia S., Koch C.A., Cass C.E., Durocher D., Weinfeld M., Glover J.N.
Mol. Cell 17:657-670(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), DOMAIN ARCHITECTURE, MUTAGENESIS OF ARG-44; LYS-45 AND ARG-48, FHA DOMAIN, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF129451 mRNA. Translation: AAF36487.1.
BC057659 mRNA. Translation: AAH57659.1.
CCDSCCDS39945.1. [Q9JLV6-1]
UniGeneMm.238254.
Mm.487968.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1UJXNMR-A1-106[»]
1YJ5X-ray2.80A/B140-522[»]
C1-143[»]
1YJMX-ray2.20A/B/C1-110[»]
3U7EX-ray1.70B142-522[»]
3U7FX-ray1.80B142-522[»]
3U7GX-ray2.10A144-522[»]
3U7HX-ray2.00B142-522[»]
3ZVLX-ray1.65A111-522[»]
3ZVMX-ray2.00A/B111-522[»]
3ZVNX-ray2.15A111-522[»]
ProteinModelPortalQ9JLV6.
SMRQ9JLV6. Positions 4-110, 143-522.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ9JLV6. 2 interactions.
MINTMINT-4108135.

PTM databases

PhosphoSiteQ9JLV6.

Proteomic databases

MaxQBQ9JLV6.
PaxDbQ9JLV6.
PRIDEQ9JLV6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

UCSCuc012fjx.1. mouse. [Q9JLV6-1]

Organism-specific databases

MGIMGI:1891698. Pnkp.

Phylogenomic databases

eggNOGCOG0241.
HOGENOMHOG000031466.
HOVERGENHBG053624.
InParanoidQ9JLV6.
PhylomeDBQ9JLV6.

Gene expression databases

CleanExMM_PNKP.
GenevestigatorQ9JLV6.

Family and domain databases

Gene3D2.60.200.20. 1 hit.
3.40.50.1000. 1 hit.
3.40.50.300. 1 hit.
InterProIPR000253. FHA_dom.
IPR023214. HAD-like_dom.
IPR006549. HAD-SF_hydro_IIIA.
IPR027417. P-loop_NTPase.
IPR013954. PNK3P.
IPR006550. PNK_3Pase_met.
IPR006551. Polynucleotide_phosphatase.
IPR008984. SMAD_FHA_domain.
[Graphical view]
PfamPF08645. PNK3P. 1 hit.
[Graphical view]
SUPFAMSSF49879. SSF49879. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF56784. SSF56784. 1 hit.
TIGRFAMsTIGR01664. DNA-3'-Pase. 1 hit.
TIGR01662. HAD-SF-IIIA. 1 hit.
TIGR01663. PNK-3'Pase. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ9JLV6.
PROQ9JLV6.
SOURCESearch...

Entry information

Entry namePNKP_MOUSE
AccessionPrimary (citable) accession number: Q9JLV6
Secondary accession number(s): Q6PFA3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: July 9, 2014
This is version 102 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot