Details for: PNKP

Gene ID: 11284

Symbol: PNKP

Ensembl ID: ENSG00000039650

Description: polynucleotide kinase 3'-phosphatase

Associated with

Cells (max top 100)

(Marker Scores and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: kidney capillary endothelial cell (CL1000892)
    Fold Change: 1.57
    Marker Score: 491
  • Cell Name: mononuclear cell (CL0000842)
    Fold Change: 1.49
    Marker Score: 480
  • Cell Name: kidney proximal straight tubule epithelial cell (CL1000839)
    Fold Change: 1.38
    Marker Score: 3,243
  • Cell Name: Leydig cell (CL0000178)
    Fold Change: 1.31
    Marker Score: 1,415
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: 1.23
    Marker Score: 19,261
  • Cell Name: early pro-B cell (CL0002046)
    Fold Change: 1.23
    Marker Score: 12,418
  • Cell Name: bladder urothelial cell (CL1001428)
    Fold Change: 1.17
    Marker Score: 1,722
  • Cell Name: lymphoid lineage restricted progenitor cell (CL0000838)
    Fold Change: 1.16
    Marker Score: 695
  • Cell Name: bronchial goblet cell (CL1000312)
    Fold Change: 1.12
    Marker Score: 555
  • Cell Name: choroid plexus epithelial cell (CL0000706)
    Fold Change: 1.1
    Marker Score: 1,012
  • Cell Name: cell in vitro (CL0001034)
    Fold Change: 1.09
    Marker Score: 37,683
  • Cell Name: placental villous trophoblast (CL2000060)
    Fold Change: 1.06
    Marker Score: 4,161
  • Cell Name: ciliated columnar cell of tracheobronchial tree (CL0002145)
    Fold Change: 1.05
    Marker Score: 9,152
  • Cell Name: acinar cell of salivary gland (CL0002623)
    Fold Change: 1.05
    Marker Score: 2,398
  • Cell Name: Bergmann glial cell (CL0000644)
    Fold Change: 1.01
    Marker Score: 413
  • Cell Name: cerebral cortex GABAergic interneuron (CL0010011)
    Fold Change: 1
    Marker Score: 71,629
  • Cell Name: forebrain radial glial cell (CL0013000)
    Fold Change: 0.99
    Marker Score: 47,853
  • Cell Name: primordial germ cell (CL0000670)
    Fold Change: 0.99
    Marker Score: 1,239
  • Cell Name: absorptive cell (CL0000212)
    Fold Change: 0.98
    Marker Score: 30,379
  • Cell Name: ovarian surface epithelial cell (CL2000064)
    Fold Change: 0.98
    Marker Score: 2,667
  • Cell Name: tonsil germinal center B cell (CL2000006)
    Fold Change: 0.97
    Marker Score: 2,889
  • Cell Name: fibroblast of cardiac tissue (CL0002548)
    Fold Change: 0.94
    Marker Score: 5,656
  • Cell Name: intestinal crypt stem cell of colon (CL0009043)
    Fold Change: 0.94
    Marker Score: 2,386
  • Cell Name: connective tissue cell (CL0002320)
    Fold Change: 0.94
    Marker Score: 243
  • Cell Name: epithelial cell of nephron (CL1000449)
    Fold Change: 0.93
    Marker Score: 1,947
  • Cell Name: tuft cell of colon (CL0009041)
    Fold Change: 0.92
    Marker Score: 475
  • Cell Name: kidney epithelial cell (CL0002518)
    Fold Change: 0.92
    Marker Score: 972
  • Cell Name: granulosa cell (CL0000501)
    Fold Change: 0.92
    Marker Score: 9,234
  • Cell Name: BEST4+ intestinal epithelial cell, human (CL4030026)
    Fold Change: 0.91
    Marker Score: 431
  • Cell Name: pancreatic acinar cell (CL0002064)
    Fold Change: 0.91
    Marker Score: 1,925
  • Cell Name: Unknown (CL0002371)
    Fold Change: 0.91
    Marker Score: 967
  • Cell Name: common dendritic progenitor (CL0001029)
    Fold Change: 0.91
    Marker Score: 314
  • Cell Name: CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell (CL0000915)
    Fold Change: 0.91
    Marker Score: 1,286
  • Cell Name: transit amplifying cell (CL0009010)
    Fold Change: 0.9
    Marker Score: 5,152
  • Cell Name: mesenchymal cell (CL0008019)
    Fold Change: 0.9
    Marker Score: 1,523
  • Cell Name: abnormal cell (CL0001061)
    Fold Change: 0.89
    Marker Score: 2,680
  • Cell Name: B-1 B cell (CL0000819)
    Fold Change: 0.89
    Marker Score: 1,557
  • Cell Name: glandular epithelial cell (CL0000150)
    Fold Change: 0.89
    Marker Score: 2,193
  • Cell Name: neural cell (CL0002319)
    Fold Change: 0.89
    Marker Score: 427
  • Cell Name: CD4-positive, alpha-beta memory T cell, CD45RO-positive (CL0001204)
    Fold Change: 0.88
    Marker Score: 5,648
  • Cell Name: myeloid leukocyte (CL0000766)
    Fold Change: 0.88
    Marker Score: 1,063
  • Cell Name: pro-T cell (CL0000827)
    Fold Change: 0.88
    Marker Score: 3,596
  • Cell Name: alpha-beta T cell (CL0000789)
    Fold Change: 0.87
    Marker Score: 662
  • Cell Name: epicardial adipocyte (CL1000309)
    Fold Change: 0.87
    Marker Score: 424
  • Cell Name: intestinal crypt stem cell of large intestine (CL0009016)
    Fold Change: 0.87
    Marker Score: 262
  • Cell Name: neoplastic cell (CL0001063)
    Fold Change: 0.87
    Marker Score: 5,290
  • Cell Name: microfold cell of epithelium of small intestine (CL1000353)
    Fold Change: 0.87
    Marker Score: 208
  • Cell Name: primitive red blood cell (CL0002355)
    Fold Change: 0.87
    Marker Score: 649
  • Cell Name: fraction A pre-pro B cell (CL0002045)
    Fold Change: 0.86
    Marker Score: 867
  • Cell Name: memory B cell (CL0000787)
    Fold Change: 0.86
    Marker Score: 651
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 0.86
    Marker Score: 309
  • Cell Name: ciliated cell (CL0000064)
    Fold Change: 0.86
    Marker Score: 2,945
  • Cell Name: IgM plasma cell (CL0000986)
    Fold Change: 0.85
    Marker Score: 297
  • Cell Name: ependymal cell (CL0000065)
    Fold Change: 0.85
    Marker Score: 297
  • Cell Name: large pre-B-II cell (CL0000957)
    Fold Change: 0.85
    Marker Score: 2,311
  • Cell Name: glandular cell of esophagus (CL0002657)
    Fold Change: 0.85
    Marker Score: 269
  • Cell Name: smooth muscle myoblast (CL0000514)
    Fold Change: 0.84
    Marker Score: 402
  • Cell Name: multi-ciliated epithelial cell (CL0005012)
    Fold Change: 0.84
    Marker Score: 1,601
  • Cell Name: plasmablast (CL0000980)
    Fold Change: 0.84
    Marker Score: 1,118
  • Cell Name: proerythroblast (CL0000547)
    Fold Change: 0.84
    Marker Score: 570
  • Cell Name: IgG-negative class switched memory B cell (CL0002117)
    Fold Change: 0.84
    Marker Score: 826
  • Cell Name: hepatocyte (CL0000182)
    Fold Change: 0.84
    Marker Score: 571
  • Cell Name: Unknown (CL0000548)
    Fold Change: 0.83
    Marker Score: 607
  • Cell Name: tendon cell (CL0000388)
    Fold Change: 0.83
    Marker Score: 204
  • Cell Name: regular ventricular cardiac myocyte (CL0002131)
    Fold Change: 0.83
    Marker Score: 18,503
  • Cell Name: naive B cell (CL0000788)
    Fold Change: 0.83
    Marker Score: 739
  • Cell Name: CD8-positive, alpha-beta cytokine secreting effector T cell (CL0000908)
    Fold Change: 0.83
    Marker Score: 357
  • Cell Name: peptic cell (CL0000155)
    Fold Change: 0.83
    Marker Score: 346
  • Cell Name: erythroid progenitor cell, mammalian (CL0001066)
    Fold Change: 0.83
    Marker Score: 265
  • Cell Name: CD4-positive helper T cell (CL0000492)
    Fold Change: 0.82
    Marker Score: 888
  • Cell Name: stromal cell of ovary (CL0002132)
    Fold Change: 0.82
    Marker Score: 9,192
  • Cell Name: hematopoietic cell (CL0000988)
    Fold Change: 0.82
    Marker Score: 542
  • Cell Name: interstitial cell of ovary (CL0002094)
    Fold Change: 0.82
    Marker Score: 5,302
  • Cell Name: mature gamma-delta T cell (CL0000800)
    Fold Change: 0.81
    Marker Score: 2,545
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: 0.81
    Marker Score: 323
  • Cell Name: regular atrial cardiac myocyte (CL0002129)
    Fold Change: 0.81
    Marker Score: 2,864
  • Cell Name: retinal pigment epithelial cell (CL0002586)
    Fold Change: 0.81
    Marker Score: 237
  • Cell Name: CD34-positive, CD38-negative hematopoietic stem cell (CL0001024)
    Fold Change: 0.8
    Marker Score: 582
  • Cell Name: lung ciliated cell (CL1000271)
    Fold Change: 0.8
    Marker Score: 381
  • Cell Name: T-helper 17 cell (CL0000899)
    Fold Change: 0.8
    Marker Score: 525
  • Cell Name: Sertoli cell (CL0000216)
    Fold Change: 0.8
    Marker Score: 4,720
  • Cell Name: decidual natural killer cell, human (CL0002343)
    Fold Change: 0.8
    Marker Score: 2,198
  • Cell Name: luminal cell of prostate epithelium (CL0002340)
    Fold Change: 0.79
    Marker Score: 462
  • Cell Name: transit amplifying cell of small intestine (CL0009012)
    Fold Change: 0.79
    Marker Score: 327
  • Cell Name: cortical cell of adrenal gland (CL0002097)
    Fold Change: 0.79
    Marker Score: 13,978
  • Cell Name: malignant cell (CL0001064)
    Fold Change: 0.79
    Marker Score: 10,566
  • Cell Name: extravillous trophoblast (CL0008036)
    Fold Change: 0.79
    Marker Score: 702
  • Cell Name: osteoclast (CL0000092)
    Fold Change: 0.78
    Marker Score: 390
  • Cell Name: stem cell (CL0000034)
    Fold Change: 0.78
    Marker Score: 1,845
  • Cell Name: early T lineage precursor (CL0002425)
    Fold Change: 0.78
    Marker Score: 593
  • Cell Name: intestinal epithelial cell (CL0002563)
    Fold Change: 0.78
    Marker Score: 1,260
  • Cell Name: epidermal cell (CL0000362)
    Fold Change: 0.78
    Marker Score: 218
  • Cell Name: type EC enteroendocrine cell (CL0000577)
    Fold Change: 0.77
    Marker Score: 728
  • Cell Name: mucous neck cell (CL0000651)
    Fold Change: 0.77
    Marker Score: 1,754
  • Cell Name: OFF retinal ganglion cell (CL4023033)
    Fold Change: 0.77
    Marker Score: 323
  • Cell Name: respiratory goblet cell (CL0002370)
    Fold Change: 0.77
    Marker Score: 222
  • Cell Name: Hofbauer cell (CL3000001)
    Fold Change: 0.77
    Marker Score: 423
  • Cell Name: smooth muscle cell of small intestine (CL1000275)
    Fold Change: 0.77
    Marker Score: 201
  • Cell Name: kidney interstitial cell (CL1000500)
    Fold Change: 0.77
    Marker Score: 545
  • Cell Name: basal cell (CL0000646)
    Fold Change: 0.77
    Marker Score: 988

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Marker Score to the Marker Score Threshold, indicating how much the gene expression has changed compared to a baseline.
Marker Score: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Marker Score to the Marker Score Threshold, indicating how much the gene expression has changed compared to a baseline.
Marker Score: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Marker Score to the Marker Score Threshold, indicating how much the gene expression has changed compared to a baseline.
Marker Score: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics:** PNKP is a bifunctional enzyme that possesses both 3'-phosphatase and kinase activities. The 3'-phosphatase activity is essential for removing the 3'-phosphate group from ap sites, while the kinase activity is necessary for the repair of DNA damage by adding a phosphate group to the 5'-end of the DNA strand. PNKP is a member of the polynucleotide kinase family and is highly conserved across species, indicating its critical role in maintaining genome integrity. **Pathways and Functions:** PNKP is involved in several key pathways, including: 1. **Apex1-independent resolution of ap sites**: PNKP is responsible for the resolution of abasic sites via the single nucleotide replacement pathway, which involves the addition of a nucleotide to fill the gap. 2. **ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity**: PNKP uses ATP to phosphorylate the 5'-end of DNA, creating a 5'-phosphate group that is essential for DNA repair. 3. **Base-excision repair**: PNKP is a key component of the base excision repair pathway, which involves the removal and replacement of damaged bases in DNA. 4. **Double-strand break repair via nonhomologous end joining**: PNKP is involved in the repair of double-strand breaks via nonhomologous end joining, which is a critical mechanism for maintaining genome stability. **Clinical Significance:** PNKP has been implicated in various diseases, including: 1. **Cancer**: Mutations in the PNKP gene have been associated with an increased risk of cancer, highlighting the importance of this enzyme in maintaining genome integrity. 2. **Neurological disorders**: PNKP has been linked to neurological disorders such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, which are characterized by DNA damage and oxidative stress. 3. **Radiation-induced diseases**: PNKP plays a critical role in the repair of DNA damage caused by radiation, and mutations in the PNKP gene can increase the susceptibility to radiation-induced diseases. 4. **Immunodeficiency disorders**: PNKP has been implicated in immunodeficiency disorders such as X-linked agammaglobulinemia, which is characterized by impaired DNA repair and immune function. In conclusion, PNKP is a crucial enzyme that plays a vital role in maintaining genome stability. Its involvement in various pathways, including base excision repair and nonhomologous end joining, highlights its importance in maintaining genome integrity. Further research is needed to fully understand the mechanisms of PNKP and its clinical significance in various diseases.

Genular Protein ID: 3299470044

Symbol: PNKP_HUMAN

Name: Bifunctional polynucleotide phosphatase/kinase

UniProtKB Accession Codes:

Q96T60 Q9BUL2 Q9P1V2 Q9UKU8 Q9UNF8 Q9UNI0

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 BRENDA 2 Bgee 1 BindingDB 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CDD 2 CORUM 1 CTD 1 ChEBI 10 ChEMBL 1 ComplexPortal 1 DEPOD 1 DMDM 1 DNASU 1 DisGeNET 1 EC 3 EMBL 8 EPD 1 Ensembl 2 EvolutionaryTrace 1 ExpressionAtlas 1 GO 26 Gene3D 3 GeneCards 1 GeneTree 1 GeneWiki 1 Genevisible 1 GenomeRNAi 1 GlyGen 1 HGNC 2 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 9 KEGG 1 MANE-Select 1 MIM 5 MINT 1 MalaCards 1 MassIVE 1 MaxQB 1 NCBI Taxonomy 1 NCBIfam 3 OMA 1 OpenTargets 1 Orphanet 3 OrthoDB 1 PANTHER 2 PDB 3 PDBsum 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 3 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 Pumba 1 RNAct 1 Reactome 1 RefSeq 1 Rhea 6 SAM 1 SIGNOR 1 SMR 1 STRING 1 SUPFAM 3 SignaLink 1 SwissPalm 1 TreeFam 1 UCSC 1 UniProtKB 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 10446192

Title: Molecular cloning of the human gene, PNKP, encoding a polynucleotide kinase 3'-phosphatase and evidence for its role in repair of DNA strand breaks caused by oxidative damage.

PubMed ID: 10446192

DOI: 10.1074/jbc.274.34.24176

PubMed ID: 10446193

Title: Molecular characterization of a human DNA kinase.

PubMed ID: 10446193

DOI: 10.1074/jbc.274.34.24187

PubMed ID: 15057824

Title: The DNA sequence and biology of human chromosome 19.

PubMed ID: 15057824

DOI: 10.1038/nature02399

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 15385968

Title: Xrcc4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV.

PubMed ID: 15385968

DOI: 10.1038/sj.emboj.7600375

PubMed ID: 17081983

Title: Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.

PubMed ID: 17081983

DOI: 10.1016/j.cell.2006.09.026

PubMed ID: 18669648

Title: A quantitative atlas of mitotic phosphorylation.

PubMed ID: 18669648

DOI: 10.1073/pnas.0805139105

PubMed ID: 19413330

Title: Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.

PubMed ID: 19413330

DOI: 10.1021/ac9004309

PubMed ID: 19690332

Title: Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.

PubMed ID: 19690332

DOI: 10.1126/scisignal.2000007

PubMed ID: 20068231

Title: Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

PubMed ID: 20068231

DOI: 10.1126/scisignal.2000475

PubMed ID: 20852255

Title: Dual modes of interaction between XRCC4 and polynucleotide kinase/phosphatase: implications for nonhomologous end joining.

PubMed ID: 20852255

DOI: 10.1074/jbc.m109.058719

PubMed ID: 21269460

Title: Initial characterization of the human central proteome.

PubMed ID: 21269460

DOI: 10.1186/1752-0509-5-17

PubMed ID: 21406692

Title: System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.

PubMed ID: 21406692

DOI: 10.1126/scisignal.2001570

PubMed ID: 22814378

Title: N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB.

PubMed ID: 22814378

DOI: 10.1073/pnas.1210303109

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

DOI: 10.1021/pr300630k

PubMed ID: 24275569

Title: An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.

PubMed ID: 24275569

DOI: 10.1016/j.jprot.2013.11.014

PubMed ID: 28453785

Title: Structural and functional characterization of the PNKP-XRCC4-LigIV DNA repair complex.

PubMed ID: 28453785

DOI: 10.1093/nar/gkx275

PubMed ID: 25728773

Title: Mutations in PNKP cause recessive ataxia with oculomotor apraxia type 4.

PubMed ID: 25728773

DOI: 10.1016/j.ajhg.2015.01.005

PubMed ID: 19155274

Title: Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK.

PubMed ID: 19155274

DOI: 10.1093/nar/gkn1086

PubMed ID: 20118933

Title: Mutations in PNKP cause microcephaly, seizures and defects in DNA repair.

PubMed ID: 20118933

DOI: 10.1038/ng.526

PubMed ID: 27232581

Title: Microcephalic primordial dwarfism in an Emirati patient with PNKP mutation.

PubMed ID: 27232581

DOI: 10.1002/ajmg.a.37766

Sequence Information:

  • Length: 521
  • Mass: 57076
  • Checksum: 22B5C94D41E62516
  • Sequence:
    • MGEVEAPGRL WLESPPGGAP PIFLPSDGQA LVLGRGPLTQ VTDRKCSRTQ VELVADPETR 
TVAVKQLGVN PSTTGTQELK PGLEGSLGVG DTLYLVNGLH PLTLRWEETR TPESQPDTPP 
GTPLVSQDEK RDAELPKKRM RKSNPGWENL EKLLVFTAAG VKPQGKVAGF DLDGTLITTR 
SGKVFPTGPS DWRILYPEIP RKLRELEAEG YKLVIFTNQM SIGRGKLPAE EFKAKVEAVV 
EKLGVPFQVL VATHAGLYRK PVTGMWDHLQ EQANDGTPIS IGDSIFVGDA AGRPANWAPG 
RKKKDFSCAD RLFALNLGLP FATPEEFFLK WPAAGFELPA FDPRTVSRSG PLCLPESRAL 
LSASPEVVVA VGFPGAGKST FLKKHLVSAG YVHVNRDTLG SWQRCVTTCE TALKQGKRVA 
IDNTNPDAAS RARYVQCARA AGVPCRCFLF TATLEQARHN NRFREMTDSS HIPVSDMVMY 
GYRKQFEAPT LAEGFSAILE IPFRLWVEPR LGRLYCQFSE G

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.