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Q9JLV6

- PNKP_MOUSE

UniProt

Q9JLV6 - PNKP_MOUSE

Protein

Bifunctional polynucleotide phosphatase/kinase

Gene

Pnkp

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 103 (01 Oct 2014)
      Sequence version 2 (19 Jul 2004)
      Previous versions | rss
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    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

    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-SubCell

    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

    MSQLGSRGRL WLQSPTGGPP PIFLPSDGQA LVLGRGPLTQ VTDRKCSRNQ    50
    VELIADPESR TVAVKQLGVN PSTVGVHELK PGLSGSLSLG DVLYLVNGLY 100
    PLTLRWEELS TSGSQPDAPP DTPGDPEEGE DTEPQKKRVR KSSLGWESLK 150
    KLLVFTASGV KPQGKVAAFD LDGTLITTRS GKVFPTSPSD WRILYPEIPK 200
    KLQELAAEGY KLVIFTNQMG IGRGKLPAEV FKGKVEAVLE KLGVPFQVLV 250
    ATHAGLNRKP VSGMWDHLQE QANEGIPISV EDSVFVGDAA GRLANWAPGR 300
    KKKDFSCADR LFALNVGLPF ATPEEFFLKW PAARFELPAF DPRTISSAGP 350
    LYLPESSSLL SPNPEVVVAV GFPGAGKSTF IQEHLVSAGY VHVNRDTLGS 400
    WQRCVSSCQA ALRQGKRVVI DNTNPDVPSR ARYIQCAKDA GVPCRCFNFC 450
    ATIEQARHNN RFREMTDPSH APVSDMVMFS YRKQFEPPTL AEGFLEILEI 500
    PFRLQEHLDP ALQRLYRQFS EG 522
    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

    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 1, 2014
    This is version 103 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