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Protein

Bifunctional polynucleotide phosphatase/kinase

Gene

Pnkp

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

A 3'-phosphopolynucleotide + H2O = a polynucleotide + phosphate.
ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi371 – 3788ATPSequence Analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Kinase, Transferase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi2.7.1.78. 3474.

Names & Taxonomyi

Protein namesi
Recommended name:
Bifunctional polynucleotide phosphatase/kinase
Alternative name(s):
DNA 5'-kinase/3'-phosphatase
Polynucleotide kinase-3'-phosphatase
Including the following 2 domains:
Polynucleotide 3'-phosphatase (EC:3.1.3.32)
Alternative name(s):
2'(3')-polynucleotidase
Polynucleotide 5'-hydroxyl-kinase (EC:2.7.1.78)
Gene namesi
Name:Pnkp
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Unplaced

Organism-specific databases

MGIiMGI:1891698. Pnkp.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi44 – 441R → A: Abrogates phosphopeptide recognition. 1 Publication
Mutagenesisi45 – 451K → N: No effect on phosphopeptide recognition. 1 Publication
Mutagenesisi48 – 481R → A: Abrogates phosphopeptide recognition. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 522522Bifunctional polynucleotide phosphatase/kinasePRO_0000058479Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity
Modified residuei114 – 1141PhosphoserineBy similarity
Modified residuei122 – 1221Phosphothreonine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ9JLV6.
PaxDbiQ9JLV6.
PRIDEiQ9JLV6.

PTM databases

PhosphoSiteiQ9JLV6.

Expressioni

Gene expression databases

CleanExiMM_PNKP.
GenevestigatoriQ9JLV6.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

IntActiQ9JLV6. 2 interactions.
MINTiMINT-4108135.

Structurei

Secondary structure

1
522
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 138Combined sources
Beta strandi16 – 183Combined sources
Turni26 – 283Combined sources
Beta strandi31 – 366Combined sources
Turni37 – 404Combined sources
Beta strandi44 – 463Combined sources
Beta strandi51 – 566Combined sources
Turni57 – 604Combined sources
Beta strandi61 – 666Combined sources
Beta strandi68 – 703Combined sources
Beta strandi73 – 786Combined sources
Beta strandi84 – 885Combined sources
Beta strandi92 – 965Combined sources
Beta strandi99 – 10810Combined sources
Beta strandi145 – 1495Combined sources
Beta strandi152 – 1565Combined sources
Beta strandi164 – 1696Combined sources
Turni172 – 1743Combined sources
Beta strandi175 – 1773Combined sources
Beta strandi179 – 1813Combined sources
Beta strandi182 – 1843Combined sources
Beta strandi192 – 1943Combined sources
Helixi198 – 20710Combined sources
Beta strandi211 – 2177Combined sources
Helixi219 – 2224Combined sources
Helixi228 – 24215Combined sources
Beta strandi247 – 2515Combined sources
Beta strandi253 – 2553Combined sources
Helixi263 – 2719Combined sources
Beta strandi273 – 2753Combined sources
Helixi280 – 2823Combined sources
Beta strandi284 – 2863Combined sources
Beta strandi297 – 2993Combined sources
Helixi308 – 3169Combined sources
Helixi323 – 3275Combined sources
Helixi342 – 3443Combined sources
Beta strandi351 – 3544Combined sources
Beta strandi366 – 3716Combined sources
Helixi377 – 3848Combined sources
Helixi386 – 3883Combined sources
Beta strandi391 – 3933Combined sources
Helixi395 – 3973Combined sources
Helixi401 – 41313Combined sources
Beta strandi418 – 4225Combined sources
Helixi427 – 44014Combined sources
Beta strandi444 – 4496Combined sources
Helixi453 – 46614Combined sources
Helixi475 – 48410Combined sources
Helixi490 – 4923Combined sources
Beta strandi495 – 5006Combined sources
Helixi510 – 5167Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliQ9JLV6.
SMRiQ9JLV6. Positions 4-110, 143-522.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9JLV6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 110105FHAAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni145 – 336192PhosphataseAdd
BLAST
Regioni340 – 517178KinaseAdd
BLAST

Domaini

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.1 Publication

Sequence similaritiesi

In the N-terminal section; belongs to the DNA 3' phosphatase family.Curated
Contains 1 FHA domain.Curated

Phylogenomic databases

eggNOGiCOG0241.
HOGENOMiHOG000031466.
HOVERGENiHBG053624.
InParanoidiQ9JLV6.
PhylomeDBiQ9JLV6.

Family and domain databases

Gene3Di2.60.200.20. 1 hit.
3.40.50.1000. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR000253. 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]
PfamiPF08645. PNK3P. 1 hit.
[Graphical view]
SUPFAMiSSF49879. SSF49879. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01664. DNA-3'-Pase. 1 hit.
TIGR01662. HAD-SF-IIIA. 1 hit.
TIGR01663. PNK-3'Pase. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9JLV6-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MSQLGSRGRL WLQSPTGGPP PIFLPSDGQA LVLGRGPLTQ VTDRKCSRNQ
60 70 80 90 100
VELIADPESR TVAVKQLGVN PSTVGVHELK PGLSGSLSLG DVLYLVNGLY
110 120 130 140 150
PLTLRWEELS TSGSQPDAPP DTPGDPEEGE DTEPQKKRVR KSSLGWESLK
160 170 180 190 200
KLLVFTASGV KPQGKVAAFD LDGTLITTRS GKVFPTSPSD WRILYPEIPK
210 220 230 240 250
KLQELAAEGY KLVIFTNQMG IGRGKLPAEV FKGKVEAVLE KLGVPFQVLV
260 270 280 290 300
ATHAGLNRKP VSGMWDHLQE QANEGIPISV EDSVFVGDAA GRLANWAPGR
310 320 330 340 350
KKKDFSCADR LFALNVGLPF ATPEEFFLKW PAARFELPAF DPRTISSAGP
360 370 380 390 400
LYLPESSSLL SPNPEVVVAV GFPGAGKSTF IQEHLVSAGY VHVNRDTLGS
410 420 430 440 450
WQRCVSSCQA ALRQGKRVVI DNTNPDVPSR ARYIQCAKDA GVPCRCFNFC
460 470 480 490 500
ATIEQARHNN RFREMTDPSH APVSDMVMFS YRKQFEPPTL AEGFLEILEI
510 520
PFRLQEHLDP ALQRLYRQFS EG
Length:522
Mass (Da):57,223
Last modified:July 19, 2004 - v2
Checksum:iC691C0A6DA9F47FE
GO
Isoform 2 (identifier: Q9JLV6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     163-191: QGKVAAFDLDGTLITTRSGKVFPTSPSDW → RA

Note: No experimental confirmation available.

Show »
Length:495
Mass (Da):54,373
Checksum:i6FE381B1531C953C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti77 – 771H → Q in AAF36487 (Ref. 1) Curated
Sequence conflicti216 – 2161Missing in AAF36487 (Ref. 1) Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei163 – 19129QGKVA…SPSDW → RA in isoform 2. 1 PublicationVSP_010771Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF129451 mRNA. Translation: AAF36487.1.
BC057659 mRNA. Translation: AAH57659.1.
CCDSiCCDS39945.1. [Q9JLV6-1]
UniGeneiMm.238254.
Mm.487968.

Genome annotation databases

UCSCiuc012fjx.1. mouse. [Q9JLV6-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF129451 mRNA. Translation: AAF36487.1.
BC057659 mRNA. Translation: AAH57659.1.
CCDSiCCDS39945.1. [Q9JLV6-1]
UniGeneiMm.238254.
Mm.487968.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliQ9JLV6.
SMRiQ9JLV6. Positions 4-110, 143-522.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9JLV6. 2 interactions.
MINTiMINT-4108135.

PTM databases

PhosphoSiteiQ9JLV6.

Proteomic databases

MaxQBiQ9JLV6.
PaxDbiQ9JLV6.
PRIDEiQ9JLV6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

UCSCiuc012fjx.1. mouse. [Q9JLV6-1]

Organism-specific databases

MGIiMGI:1891698. Pnkp.

Phylogenomic databases

eggNOGiCOG0241.
HOGENOMiHOG000031466.
HOVERGENiHBG053624.
InParanoidiQ9JLV6.
PhylomeDBiQ9JLV6.

Enzyme and pathway databases

BRENDAi2.7.1.78. 3474.

Miscellaneous databases

EvolutionaryTraceiQ9JLV6.
PROiQ9JLV6.
SOURCEiSearch...

Gene expression databases

CleanExiMM_PNKP.
GenevestigatoriQ9JLV6.

Family and domain databases

Gene3Di2.60.200.20. 1 hit.
3.40.50.1000. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR000253. 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]
PfamiPF08645. PNK3P. 1 hit.
[Graphical view]
SUPFAMiSSF49879. SSF49879. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01664. DNA-3'-Pase. 1 hit.
TIGR01662. HAD-SF-IIIA. 1 hit.
TIGR01663. PNK-3'Pase. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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. Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), DOMAIN ARCHITECTURE, MUTAGENESIS OF ARG-44; LYS-45 AND ARG-48, FHA DOMAIN, SUBUNIT.

Entry informationi

Entry nameiPNKP_MOUSE
AccessioniPrimary (citable) accession number: Q9JLV6
Secondary accession number(s): Q6PFA3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: May 27, 2015
This is version 110 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.