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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)DescriptionActionsGraphical viewLength
Nucleotide bindingi371 – 378ATPSequence analysis8

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
Proteomesi
  • UP000000589 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)DescriptionActionsGraphical viewLength
Mutagenesisi44R → A: Abrogates phosphopeptide recognition. 1 Publication1
Mutagenesisi45K → N: No effect on phosphopeptide recognition. 1 Publication1
Mutagenesisi48R → A: Abrogates phosphopeptide recognition. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000584791 – 522Bifunctional polynucleotide phosphatase/kinaseAdd BLAST522

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineBy similarity1
Modified residuei114PhosphoserineBy similarity1
Modified residuei122PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9JLV6.
PaxDbiQ9JLV6.
PeptideAtlasiQ9JLV6.
PRIDEiQ9JLV6.

PTM databases

iPTMnetiQ9JLV6.
PhosphoSitePlusiQ9JLV6.

Expressioni

Gene expression databases

CleanExiMM_PNKP.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

IntActiQ9JLV6. 2 interactors.
MINTiMINT-4108135.
STRINGi10090.ENSMUSP00000003044.

Structurei

Secondary structure

1522
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 13Combined sources8
Beta strandi16 – 18Combined sources3
Turni26 – 28Combined sources3
Beta strandi31 – 36Combined sources6
Turni37 – 40Combined sources4
Beta strandi44 – 46Combined sources3
Beta strandi51 – 56Combined sources6
Turni57 – 60Combined sources4
Beta strandi61 – 66Combined sources6
Beta strandi68 – 70Combined sources3
Beta strandi73 – 78Combined sources6
Beta strandi84 – 88Combined sources5
Beta strandi92 – 96Combined sources5
Beta strandi99 – 108Combined sources10
Beta strandi145 – 149Combined sources5
Beta strandi152 – 156Combined sources5
Beta strandi164 – 169Combined sources6
Turni172 – 174Combined sources3
Beta strandi175 – 177Combined sources3
Beta strandi179 – 181Combined sources3
Beta strandi182 – 184Combined sources3
Beta strandi192 – 194Combined sources3
Helixi198 – 207Combined sources10
Beta strandi211 – 217Combined sources7
Helixi219 – 222Combined sources4
Helixi228 – 242Combined sources15
Beta strandi247 – 251Combined sources5
Beta strandi253 – 255Combined sources3
Helixi263 – 271Combined sources9
Beta strandi273 – 275Combined sources3
Helixi280 – 282Combined sources3
Beta strandi284 – 286Combined sources3
Beta strandi297 – 299Combined sources3
Helixi308 – 316Combined sources9
Helixi323 – 327Combined sources5
Helixi342 – 344Combined sources3
Beta strandi351 – 354Combined sources4
Beta strandi366 – 371Combined sources6
Helixi377 – 384Combined sources8
Helixi386 – 388Combined sources3
Beta strandi391 – 393Combined sources3
Helixi395 – 397Combined sources3
Helixi401 – 413Combined sources13
Beta strandi418 – 422Combined sources5
Helixi427 – 440Combined sources14
Beta strandi444 – 449Combined sources6
Helixi453 – 466Combined sources14
Helixi475 – 484Combined sources10
Helixi490 – 492Combined sources3
Beta strandi495 – 500Combined sources6
Helixi510 – 516Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9JLV6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini6 – 110FHAAdd BLAST105

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni145 – 336PhosphataseAdd BLAST192
Regioni340 – 517KinaseAdd BLAST178

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

eggNOGiKOG2134. Eukaryota.
COG0241. LUCA.
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)DescriptionActionsGraphical viewLength
Sequence conflicti77H → Q in AAF36487 (Ref. 1) Curated1
Sequence conflicti216Missing in AAF36487 (Ref. 1) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_010771163 – 191QGKVA…SPSDW → RA in isoform 2. 1 PublicationAdd BLAST29

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9JLV6. 2 interactors.
MINTiMINT-4108135.
STRINGi10090.ENSMUSP00000003044.

PTM databases

iPTMnetiQ9JLV6.
PhosphoSitePlusiQ9JLV6.

Proteomic databases

EPDiQ9JLV6.
PaxDbiQ9JLV6.
PeptideAtlasiQ9JLV6.
PRIDEiQ9JLV6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

UCSCiuc012fjx.1. mouse. [Q9JLV6-1]

Organism-specific databases

MGIiMGI:1891698. Pnkp.

Phylogenomic databases

eggNOGiKOG2134. Eukaryota.
COG0241. LUCA.
HOGENOMiHOG000031466.
HOVERGENiHBG053624.
InParanoidiQ9JLV6.
PhylomeDBiQ9JLV6.

Enzyme and pathway databases

BRENDAi2.7.1.78. 3474.

Miscellaneous databases

EvolutionaryTraceiQ9JLV6.
PROiQ9JLV6.
SOURCEiSearch...

Gene expression databases

CleanExiMM_PNKP.

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...

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: November 2, 2016
This is version 121 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

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 one 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.