Gene description for PNKP
Gene name polynucleotide kinase 3'-phosphatase
Gene symbol PNKP
Other names/aliases AOA4
EIEE10
MCSZ
PNK
Species Homo sapiens
 Database cross references - PNKP
ExoCarta ExoCarta_11284
Vesiclepedia VP_11284
Entrez Gene 11284
HGNC 9154
MIM 605610
UniProt Q96T60  
 PNKP identified in exosomes derived from the following tissue/cell type
Colorectal cancer cells 23161513    
Colorectal cancer cells 23161513    
Colorectal cancer cells 23161513    
Hepatocytes 26054723    
Mesenchymal stem cells 36408942    
Thymus 23844026    
 Gene ontology annotations for PNKP
Molecular Function
    purine nucleotide binding GO:0017076 NAS
    ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity GO:0046404 IDA
    nucleotide kinase activity GO:0019201 IDA
    double-stranded DNA binding GO:0003690 TAS
    protein binding GO:0005515 IPI
    ATP binding GO:0005524 NAS
    damaged DNA binding GO:0003684 NAS
    polynucleotide 3'-phosphatase activity GO:0046403 IDA
    endonuclease activity GO:0004519 NAS
Biological Process
    polynucleotide 3' dephosphorylation GO:0098506 IEA
    DNA-dependent DNA replication GO:0006261 NAS
    DNA damage response, detection of DNA damage GO:0042769 NAS
    DNA 3' dephosphorylation involved in DNA repair GO:0098504 IBA
    response to oxidative stress GO:0006979 IDA
    nucleotide-excision repair, DNA damage removal GO:0000718 NAS
    nucleic acid phosphodiester bond hydrolysis GO:0090305 NAS
    DNA repair GO:0006281 TAS
    nucleotide phosphorylation GO:0046939 IDA
    dephosphorylation GO:0016311 IDA
    base-excision repair GO:0006284 TAS
    response to radiation GO:0009314 TAS
Subcellular Localization
    membrane GO:0016020 IDA
    nucleoplasm GO:0005654 TAS
    nucleus GO:0005634 IDA
    nucleolus GO:0005730 IDA
 Experiment description of studies that identified PNKP in exosomes
1
Experiment ID 207
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|HSP70|FLOT1
Enriched markers
✔
VDAC
Negative markers
✔
NTA
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23161513    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS.
Authors Demory Beckler M, Higginbotham JN, Franklin JL, Ham AJ, Halvey PJ, Imasuen IE, Whitwell C, Li M, Liebler DC, Coffey RJ.
Journal name Mol Cell Proteomics
Publication year 2012
Sample Colorectal cancer cells
Sample name DKO-1
Isolation/purification methods Differential centrifugation
Filtration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
2
Experiment ID 208
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|HSP70|FLOT1
Enriched markers
✔
VDAC
Negative markers
✔
NTA
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23161513    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS.
Authors Demory Beckler M, Higginbotham JN, Franklin JL, Ham AJ, Halvey PJ, Imasuen IE, Whitwell C, Li M, Liebler DC, Coffey RJ.
Journal name Mol Cell Proteomics
Publication year 2012
Sample Colorectal cancer cells
Sample name Dks-8
Isolation/purification methods Differential centrifugation
Filtration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
3
Experiment ID 209
MISEV standards
✘ Biophysical techniques
✔
TSG101|HSP70|FLOT1
Enriched markers
✔
VDAC
Negative markers
✔
NTA
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23161513    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS.
Authors Demory Beckler M, Higginbotham JN, Franklin JL, Ham AJ, Halvey PJ, Imasuen IE, Whitwell C, Li M, Liebler DC, Coffey RJ.
Journal name Mol Cell Proteomics
Publication year 2012
Sample Colorectal cancer cells
Sample name DLD-1
Isolation/purification methods Differential centrifugation
Filtration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
4
Experiment ID 237
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|Alix|HSC70|GAPDH
Enriched markers
✔
HSP90B1
Negative markers
✔
qNano
Particle analysis
Identified molecule mRNA
Identification method RNA Sequencing
PubMed ID 26054723    
Organism Homo sapiens
Experiment description Hepatocellular carcinoma-derived exosomes promote motility of immortalized hepatocyte through transfer of oncogenic proteins and RNAs
Authors He M, Qin H, Poon TC, Sze SC, Ding X, Co NN, Ngai SM, Chan TF, Wong N
Journal name Carcinogenesis
Publication year 2015
Sample Hepatocytes
Sample name MIHA
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
RNA
Methods used in the study Western blotting
Mass spectrometry
RNA Sequencing
5
Experiment ID 488
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD81|CD63|GAPDH|SDCBP|LAMP1|TFRC|UCHL1|FLOT2|LAMP2|FLOT1|ICAM1|RAB5B|CD151|RAB35|TSG101|RAB5A|CD82
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Homo sapiens
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Mesenchymal stem cells
Sample name UCMSC
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
6
Experiment ID 217
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|CD81|CD9|CD63
Enriched markers
✘ Negative markers
✔
NTA
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23844026    
Organism Homo sapiens
Experiment description Characterization of human thymic exosomes.
Authors Skogberg G, Gudmundsdottir J, van der Post S, Sandstrom K, Bruhn S, Benson M, Mincheva-Nilsson L, Baranov V, Telemo E, Ekwall O.
Journal name PLoS One
Publication year 2013
Sample Thymus
Sample name Normal-Thymus
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
 Protein-protein interactions for PNKP
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 XRCC4  
Affinity Capture-MS Homo sapiens
2 NUP93 9688
Affinity Capture-MS Homo sapiens
3 YWHAQ 10971
Affinity Capture-MS Homo sapiens
4 LIG4 3981
Affinity Capture-MS Homo sapiens
5 MCM3 4172
Affinity Capture-MS Homo sapiens
6 SMAD5 4090
Affinity Capture-MS Homo sapiens
7 XRCC1 7515
Invitro Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
8 KRTAP4-12  
Two-hybrid Homo sapiens
9 TRIM37  
Two-hybrid Homo sapiens
10 DDX20 11218
Affinity Capture-MS Homo sapiens
11 MYOZ1  
Two-hybrid Homo sapiens
12 NOL3 8996
Affinity Capture-MS Homo sapiens
13 LIG3 3980
Affinity Capture-MS Homo sapiens
14 DNAAF5 54919
Affinity Capture-MS Homo sapiens
15 SLC25A12 8604
Affinity Capture-MS Homo sapiens
16 NOM1  
Affinity Capture-MS Homo sapiens
17 LAS1L 81887
Affinity Capture-MS Homo sapiens
18 MAGEA11  
Two-hybrid Homo sapiens
19 ATAD3B 83858
Affinity Capture-MS Homo sapiens
View the network image/svg+xml
 Pathways in which PNKP is involved
PathwayEvidenceSource
APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway TAS Reactome





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