Gene description for Phgdh
Gene name 3-phosphoglycerate dehydrogenase
Gene symbol Phgdh
Other names/aliases 3-PGDH
3PGDH
4930479N23
A10
PGAD
PGD
PGDH
SERA
Species Mus musculus
 Database cross references - Phgdh
ExoCarta ExoCarta_236539
Vesiclepedia VP_236539
Entrez Gene 236539
UniProt Q61753  
 Phgdh identified in sEVs derived from the following tissue/cell type
Brain cancer cells 19109410    
Colon cancer cells 37309723    
Fibroblasts 23260141    
Macrophages 23658846    
Macrophages 23658846    
Macrophages 23658846    
Neural stem cells 25242146    
T-cell lymphoma cells 37309723    
 Gene ontology annotations for Phgdh
Molecular Function
    phosphoglycerate dehydrogenase activity GO:0004617 IBA
    phosphoglycerate dehydrogenase activity GO:0004617 ISO
    phosphoglycerate dehydrogenase activity GO:0004617 TAS
    NAD binding GO:0051287 IEA
Biological Process
    glutamine metabolic process GO:0006541 IMP
    glycine metabolic process GO:0006544 IMP
    L-serine metabolic process GO:0006563 IMP
    L-serine biosynthetic process GO:0006564 IEA
    threonine metabolic process GO:0006566 IMP
    gamma-aminobutyric acid metabolic process GO:0009448 IMP
    regulation of gene expression GO:0010468 IMP
    taurine metabolic process GO:0019530 IMP
    spinal cord development GO:0021510 IMP
    glial cell development GO:0021782 IMP
    neural tube development GO:0021915 IMP
    neurogenesis GO:0022008 IMP
    neuron projection development GO:0031175 IMP
    G1 to G0 transition GO:0070314 IMP
Subcellular Localization
    myelin sheath GO:0043209 HDA
 Experiment description of studies that identified Phgdh in sEVs
1
Experiment ID 26
MISEV standards
✔
EM
Biophysical techniques
✔
Alix|GAPDH|HSP70|CD9
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 19109410    
Organism Mus musculus
Experiment description Proteomic and immunologic analyses of brain tumor exosomes.
Authors "Graner MW, Alzate O, Dechkovskaia AM, Keene JD, Sampson JH, Mitchell DA, Bigner DD"
Journal name FASEB
Publication year 2008
Sample Brain cancer cells
Sample name SMA560vIII
Isolation/purification methods Differential centrifugation
Sucrose density gradient
Flotation density 1.13-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry [MALDI TOF/TOF]
Western blotting
2
Experiment ID 907
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample Colon cancer cells
Sample name C26
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
3
Experiment ID 210
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|FLOT1
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23260141    
Organism Mus musculus
Experiment description Exosomes Mediate Stromal Mobilization of Autocrine Wnt-PCP Signaling in Breast Cancer Cell Migration.
Authors "Luga V, Zhang L, Viloria-Petit AM, Ogunjimi AA, Inanlou MR, Chiu E, Buchanan M, Hosein AN, Basik M, Wrana JL."
Journal name Cell
Publication year 2012
Sample Fibroblasts
Sample name Normal-Fibroblasts (L cells)
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
4
Experiment ID 214
MISEV standards
✔
EM
Biophysical techniques
✘ Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23658846    
Organism Mus musculus
Experiment description Immunomodulatory impact of leishmania-induced macrophage exosomes: a comparative proteomic and functional analysis.
Authors "Hassani K, Olivier M."
Journal name PLoS Negl Trop Dis
Publication year 2013
Sample Macrophages
Sample name Leishmania-infected-Macrophage (J774A.1)
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Filtration
Protease inhibitors
Sucrose density gradient
Filtration
Ultracentrifugation
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
5
Experiment ID 215
MISEV standards
✔
EM
Biophysical techniques
✘ Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23658846    
Organism Mus musculus
Experiment description Immunomodulatory impact of leishmania-induced macrophage exosomes: a comparative proteomic and functional analysis.
Authors "Hassani K, Olivier M."
Journal name PLoS Negl Trop Dis
Publication year 2013
Sample Macrophages
Sample name LPS-treated-Macrophage (J774A.1)
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Filtration
Protease inhibitors
Sucrose density gradient
Filtration
Ultracentrifugation
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
6
Experiment ID 216
MISEV standards
✔
EM
Biophysical techniques
✘ Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23658846    
Organism Mus musculus
Experiment description Immunomodulatory impact of leishmania-induced macrophage exosomes: a comparative proteomic and functional analysis.
Authors "Hassani K, Olivier M."
Journal name PLoS Negl Trop Dis
Publication year 2013
Sample Macrophages
Sample name Normal-Macrophage (J774A.1)
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Filtration
Protease inhibitors
Sucrose density gradient
Filtration
Ultracentrifugation
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
7
Experiment ID 264
MISEV standards
✘ Biophysical techniques
✔
CD63|CD9
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25242146    
Organism Mus musculus
Experiment description Extracellular Vesicles from Neural Stem Cells Transfer IFN-? via Ifngr1 to Activate Stat1 Signaling in Target Cells
Authors "Chiara Cossetti, Nunzio Iraci, Tim R. Mercer, Tommaso Leonardi, Emanuele Alpi, Denise Drago, Clara Alfaro-Cervello, Harpreet K. Saini, Matthew P. Davis, Julia Schaeffer, Beatriz Vega, Matilde Stefanini, CongJian Zhao, Werner Muller, Jose Manuel Garcia-Verdugo, Suresh Mathivanan, Angela Bachi, Anton J. Enright, John S. Mattick, Stefano Pluchino"
Journal name Molecular Cell
Publication year 2014
Sample Neural stem cells
Sample name NPCs - Th2 treated
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.13-1.20 g/mL
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
8
Experiment ID 908
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample T-cell lymphoma cells
Sample name EL4
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
 Protein-protein interactions for Phgdh
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 Kctd13  
Affinity Capture-MS Mus musculus
2 Mettl21e  
Affinity Capture-MS Mus musculus
3 Ubc  
Reconstituted Complex Mus musculus
4 Tmem173  
Proximity Label-MS Mus musculus
5 Eed  
Affinity Capture-MS Mus musculus
6 Mapt  
Affinity Capture-MS Mus musculus
7 Atg16l1  
Affinity Capture-MS Mus musculus
8 Rpap3  
Co-fractionation Mus musculus
9 Dok1  
Affinity Capture-MS Mus musculus
10 Fancd2  
Affinity Capture-MS Mus musculus
11 Kcnma1  
Affinity Capture-MS Mus musculus
View the network image/svg+xml
 Pathways in which Phgdh is involved
PathwayEvidenceSource
Metabolism IEA Reactome
Metabolism of amino acids and derivatives IEA Reactome
Serine biosynthesis IEA Reactome





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