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
    damaged DNA binding GO:0003684 NAS
    double-stranded DNA binding GO:0003690 TAS
    endonuclease activity GO:0004519 NAS
    protein binding GO:0005515 IPI
    ATP binding GO:0005524 NAS
    purine nucleotide binding GO:0017076 NAS
    polynucleotide 3'-phosphatase activity GO:0046403 IBA
    polynucleotide 3'-phosphatase activity GO:0046403 IDA
    polynucleotide 3'-phosphatase activity GO:0046403 TAS
    ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity GO:0046404 IBA
    ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity GO:0046404 IDA
Biological Process
    DNA-templated DNA replication GO:0006261 NAS
    DNA repair GO:0006281 IBA
    DNA repair GO:0006281 IGI
    base-excision repair, gap-filling GO:0006287 TAS
    nucleotide-excision repair GO:0006289 TAS
    double-strand break repair via nonhomologous end joining GO:0006303 IDA
    response to oxidative stress GO:0006979 IDA
    response to radiation GO:0009314 NAS
    response to radiation GO:0009314 TAS
    negative regulation of protein ADP-ribosylation GO:0010836 IMP
    positive regulation of telomere maintenance GO:0032206 IMP
    DNA ligation involved in DNA repair GO:0051103 IDA
    positive regulation of double-strand break repair via nonhomologous end joining GO:2001034 IMP
Subcellular Localization
    nucleus GO:0005634 IBA
    nucleus GO:0005634 IDA
    nucleoplasm GO:0005654 IDA
    nucleoplasm GO:0005654 TAS
    nucleolus GO:0005730 IDA
    membrane GO:0016020 HDA
    site of double-strand break GO:0035861 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 ZBTB14  
Two-hybrid Homo sapiens
2 HIST2H2BE 8349
Affinity Capture-MS Homo sapiens
3 LIG4 3981
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
4 MCM3 4172
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
5 HAP1  
Affinity Capture-Western Homo sapiens
6 SMAD5 4090
Two-hybrid Homo sapiens
7 HBB 3043
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
8 TNIP1 10318
Two-hybrid Homo sapiens
9 FOXO3  
Affinity Capture-MS Homo sapiens
10 C6orf62 81688
Affinity Capture-MS Homo sapiens
11 BCKDK 10295
Co-fractionation Homo sapiens
12 LIG3 3980
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-Western Homo sapiens
13 DNAAF5 54919
Affinity Capture-MS Homo sapiens
14 LAS1L 81887
Affinity Capture-MS Homo sapiens
15 UBE2O 63893
Affinity Capture-MS Homo sapiens
16 Cebpb  
Affinity Capture-Western Rattus norvegicus
17 HIST1H4A 8359
Affinity Capture-MS Homo sapiens
18 PPIE 10450
Affinity Capture-MS Homo sapiens
19 XRCC4  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
20 MCM5 4174
Affinity Capture-MS Homo sapiens
21 RPA2 6118
Affinity Capture-MS Homo sapiens
22 NF2 4771
Affinity Capture-MS Homo sapiens
23 ATAD3B 83858
Affinity Capture-MS Homo sapiens
24 RPA1 6117
Affinity Capture-MS Homo sapiens
25 NOLC1 9221
Affinity Capture-MS Homo sapiens
26 HBA2 3040
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
27 FOXA1  
Affinity Capture-MS Homo sapiens
28 AGTPBP1  
Affinity Capture-MS Homo sapiens
29 MYOZ1  
Two-hybrid Homo sapiens
30 MAGEA11  
Two-hybrid Homo sapiens
31 TRIM26 7726
Affinity Capture-MS Homo sapiens
32 DCPS 28960
Co-fractionation Homo sapiens
33 CREBBP  
Affinity Capture-Western Homo sapiens
34 PARK2  
Affinity Capture-MS Homo sapiens
35 NOM1  
Affinity Capture-MS Homo sapiens
36 SUV39H1  
Two-hybrid Homo sapiens
37 IKZF1  
Two-hybrid Homo sapiens
38 GEMIN4 50628
Affinity Capture-MS Homo sapiens
39 POLR2A 5430
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
40 BRD3 8019
Affinity Capture-MS Homo sapiens
41 APP 351
Reconstituted Complex Homo sapiens
42 MID1 4281
Co-fractionation Homo sapiens
43 ZNF639  
Two-hybrid Homo sapiens
44 HTT 3064
Affinity Capture-Western Homo sapiens
Co-localization Homo sapiens
Affinity Capture-Western Homo sapiens
45 CCDC43 124808
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
46 EIF4ENIF1 56478
Two-hybrid Homo sapiens
47 XRCC1 7515
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Far Western Homo sapiens
Affinity Capture-MS Homo sapiens
48 KRTAP4-12  
Two-hybrid Homo sapiens
49 TRIM37  
Two-hybrid Homo sapiens
50 DDX20 11218
Affinity Capture-MS Homo sapiens
51 VPRBP 9730
Affinity Capture-MS Homo sapiens
52 BRD4 23476
Affinity Capture-MS Homo sapiens
53 NRD1 4898
Affinity Capture-MS Homo sapiens
54 RPA3 6119
Affinity Capture-MS Homo sapiens
55 SBDS 51119
Co-fractionation Homo sapiens
56 NTRK1 4914
Affinity Capture-MS Homo sapiens
57 CDK11B 984
Affinity Capture-MS Homo sapiens
58 CAMK2A 815
Affinity Capture-MS Homo sapiens
59 C18orf25 147339
Affinity Capture-MS Homo sapiens
60 CIT 11113
Affinity Capture-MS Homo sapiens
61 Htatsf1  
Two-hybrid Mus musculus
62 KDM1A 23028
Two-hybrid Homo sapiens
63 XRCC6 2547
Affinity Capture-MS Homo sapiens
64 YWHAQ 10971
Affinity Capture-MS Homo sapiens
65 TCOF1 6949
Affinity Capture-MS Homo sapiens
66 PARP1 142
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
67 HNRNPU 3192
Affinity Capture-MS Homo sapiens
68 GZMK  
Two-hybrid Homo sapiens
69 NUP93 9688
Affinity Capture-MS Homo sapiens
70 ATXN3 4287
Affinity Capture-Western Homo sapiens
Co-localization Homo sapiens
Affinity Capture-Western Homo sapiens
71 POLB 5423
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Two-hybrid Homo sapiens
72 SSRP1 6749
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
73 NOL3 8996
Affinity Capture-MS Homo sapiens
74 SLC25A12 8604
Affinity Capture-MS Homo sapiens
75 EMX2  
Affinity Capture-MS Homo sapiens
76 ACTA2 59
Affinity Capture-MS Homo sapiens
77 SUPT16H 11198
Affinity Capture-MS Homo sapiens
78 TAF4 6874
Affinity Capture-Western Homo sapiens
79 XRCC5 7520
Affinity Capture-MS Homo sapiens
80 PRKDC 5591
Affinity Capture-MS Homo sapiens
81 EED  
Affinity Capture-MS Homo sapiens
82 OGT 8473
Reconstituted Complex Homo sapiens
83 NASP 4678
Affinity Capture-MS Homo sapiens
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