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Q9JLV6

- PNKP_MOUSE

UniProt

Q9JLV6 - PNKP_MOUSE

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Protein

Bifunctional polynucleotide phosphatase/kinase

Gene

Pnkp

Organism
Mus musculus (Mouse)
Status
Reviewed - 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

  1. ATP binding Source: UniProtKB-KW
  2. ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity Source: UniProtKB-EC
  3. polynucleotide 3'-phosphatase activity Source: UniProtKB-EC

GO - Biological processi

  1. DNA repair Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Kinase, Transferase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

ATP-binding, Nucleotide-binding

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: Unplaced

Organism-specific databases

MGIiMGI:1891698. Pnkp.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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. Align

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. 1 PublicationCurated
Sequence conflicti216 – 2161Missing in AAF36487. 1 PublicationCurated

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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
AF129451 mRNA. Translation: AAF36487.1 .
BC057659 mRNA. Translation: AAH57659.1 .
CCDSi CCDS39945.1. [Q9JLV6-1 ]
UniGenei Mm.238254.
Mm.487968.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1UJX NMR - A 1-106 [» ]
1YJ5 X-ray 2.80 A/B 140-522 [» ]
C 1-143 [» ]
1YJM X-ray 2.20 A/B/C 1-110 [» ]
3U7E X-ray 1.70 B 142-522 [» ]
3U7F X-ray 1.80 B 142-522 [» ]
3U7G X-ray 2.10 A 144-522 [» ]
3U7H X-ray 2.00 B 142-522 [» ]
3ZVL X-ray 1.65 A 111-522 [» ]
3ZVM X-ray 2.00 A/B 111-522 [» ]
3ZVN X-ray 2.15 A 111-522 [» ]
ProteinModelPortali Q9JLV6.
SMRi Q9JLV6. Positions 4-110, 143-522.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi Q9JLV6. 2 interactions.
MINTi MINT-4108135.

PTM databases

PhosphoSitei Q9JLV6.

Proteomic databases

MaxQBi Q9JLV6.
PaxDbi Q9JLV6.
PRIDEi Q9JLV6.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

UCSCi uc012fjx.1. mouse. [Q9JLV6-1 ]

Organism-specific databases

MGIi MGI:1891698. Pnkp.

Phylogenomic databases

eggNOGi COG0241.
HOGENOMi HOG000031466.
HOVERGENi HBG053624.
InParanoidi Q9JLV6.
PhylomeDBi Q9JLV6.

Miscellaneous databases

EvolutionaryTracei Q9JLV6.
PROi Q9JLV6.
SOURCEi Search...

Gene expression databases

CleanExi MM_PNKP.
Genevestigatori Q9JLV6.

Family and domain databases

Gene3Di 2.60.200.20. 1 hit.
3.40.50.1000. 1 hit.
3.40.50.300. 1 hit.
InterProi IPR000253. 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 ]
Pfami PF08645. PNK3P. 1 hit.
[Graphical view ]
SUPFAMi SSF49879. SSF49879. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF56784. SSF56784. 1 hit.
TIGRFAMsi TIGR01664. DNA-3'-Pase. 1 hit.
TIGR01662. HAD-SF-IIIA. 1 hit.
TIGR01663. PNK-3'Pase. 1 hit.
ProtoNeti Search...

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: October 29, 2014
This is version 104 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