• Gene id: 26227

Gene Summary

• Gene Symbol: PHGDH   Gene   UCSC   Ensembl
• Aliases: 3-PGDH, 3PGDH, HEL-S-113, NLS, NLS1, PDG, PGAD, PGD, PGDH, PHGDHD, SERA
• Gene name: phosphoglycerate dehydrogenase
• Alternate names: D-3-phosphoglycerate dehydrogenase, 2-oxoglutarate reductase, 3-phosphoglycerate dehydrogenase, epididymis secretory protein Li 113, malate dehydrogenase,
• Gene location: 1p12 (119711933: 119744217)     Exons: 16     NC_000001.11
• Gene summary(Entrez): This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms homotetramers for activity. Mut
• OMIM: 606879

Protein Summary

• Protein general information: O43175  
  • Name: D 3 phosphoglycerate dehydrogenase (3 PGDH) (EC 1.1.1.95) (2 oxoglutarate reductase) (EC 1.1.1.399) (Malate dehydrogenase) (EC 1.1.1.37)
  • Length: 533  
  • Mass: 56651
• Sequence:

  MAFANLRKVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKLQVVGR
  AGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLGI
  LGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDNTFAQC
  KKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIA
  VQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMRAWAGSPKGTIQVITQGTSLKNAGNCLSPAVI
  VGLLKEASKQADVNLVNAKLLVKEAGLNVTTSHSPAAPGEQGFGECLLAVALAGAPYQAVGLVQGTTPVLQGLNG
  AVFRPEVPLRRDLPLLLFRTQTSDPAMLPTMIGLLAEAGVRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHV
  TEAFQFHF

• Structural information:
  • Interpro: IPR029009  IPR006139  IPR029753  IPR029752  IPR006140   IPR036291  IPR006236  
  • Prosite: PS00065 PS00670 PS00671
  • PDB: 2G76 5N53 5N6C 5NZO 5NZP 5NZQ 5OFM 5OFV 5OFW 6CWA 6PLF 6PLG 6RIH 6RJ2 6RJ3 6RJ5 6RJ6
  • PDBsum: 2G76 5N53 5N6C 5NZO 5NZP 5NZQ 5OFM 5OFV 5OFW 6CWA 6PLF 6PLG 6RIH 6RJ2 6RJ3 6RJ5 6RJ6
  • STRING: ENSP00000358417
• Other Databases: GeneCards:  PHGDH  Malacards:  PHGDH

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0004617	phosphoglycerate dehydrogenase activity	IBA	molecular function
GO:0006520	cellular amino acid metabolic process	IBA	biological process
GO:0055114	oxidation-reduction process	IEA	biological process
GO:0004617	phosphoglycerate dehydrogenase activity	IEA	molecular function
GO:0006564	L-serine biosynthetic process	IEA	biological process
GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	IEA	molecular function
GO:0051287	NAD binding	IEA	molecular function
GO:0008652	cellular amino acid biosynthetic process	IEA	biological process
GO:0055114	oxidation-reduction process	IEA	biological process
GO:0016491	oxidoreductase activity	IEA	molecular function
GO:0006564	L-serine biosynthetic process	IEA	biological process
GO:0004617	phosphoglycerate dehydrogenase activity	TAS	molecular function
GO:0007420	brain development	TAS	biological process
GO:0030060	L-malate dehydrogenase activity	IEA	molecular function
GO:0004617	phosphoglycerate dehydrogenase activity	IEA	molecular function
GO:0006564	L-serine biosynthetic process	TAS	biological process
GO:0005829	cytosol	TAS	cellular component
GO:0070314	G1 to G0 transition	IEA	biological process
GO:0031175	neuron projection development	IEA	biological process
GO:0022008	neurogenesis	IEA	biological process
GO:0021915	neural tube development	IEA	biological process
GO:0021782	glial cell development	IEA	biological process
GO:0021510	spinal cord development	IEA	biological process
GO:0019530	taurine metabolic process	IEA	biological process
GO:0006544	glycine metabolic process	IEA	biological process
GO:0010468	regulation of gene expression	IEA	biological process
GO:0009448	gamma-aminobutyric acid metabolic process	IEA	biological process
GO:0006566	threonine metabolic process	IEA	biological process
GO:0006563	L-serine metabolic process	IEA	biological process
GO:0006541	glutamine metabolic process	IEA	biological process
GO:0004617	phosphoglycerate dehydrogenase activity	IEA	molecular function
GO:0022900	electron transport chain	IEA	biological process
GO:0009055	electron transfer activity	TAS	molecular function
GO:0070062	extracellular exosome	HDA	cellular component
GO:0070062	extracellular exosome	HDA	cellular component
GO:0070062	extracellular exosome	HDA	cellular component
GO:0070062	extracellular exosome	HDA	cellular component

KEGG pathways

Pathway id	Pathway name
hsa01100	Metabolic pathways
hsa01200	Carbon metabolism
hsa01230	Biosynthesis of amino acids
hsa00270	Cysteine and methionine metabolism
hsa00260	Glycine, serine and threonine metabolism

Diseases

Associated diseases	References
3-Phosphoglycerate dehydrogenase	KEGG:H01079
Neu-Laxova syndrome	KEGG:H02117
3-Phosphoglycerate dehydrogenase	KEGG:H01079
Neu-Laxova syndrome	KEGG:H02117
Amino acid metabolic disorder	PMID:11055895
Teratozoospermia	MIK: 17327269

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
17327269	Teratozoospermia			19 (6 controls, 13 cases)	Male infertility	GSE6872 analyzed by GEO2R (cutoff 1.5 fold)