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FLASH GENE
Symbol PHGDH contributors: mct - updated : 18-06-2016
HGNC name phosphoglycerate dehydrogenase
HGNC id 8923
Corresponding disease
NELAS Neu-Laxova syndrome
PHGDH phosphoglycerate dehydrogenase deficiency
Location 1p12      Physical location : 120.254.418 - 120.286.848
Synonym name
  • -phosphoglycerate dehydrogenase
  • D-3-phosphoglycerate
    • Synonym symbol(s) PGD, PGAD, PGDH, SERA, PDG, 3PGDH, 3-PGDH, MGC3017, SERA
    EC.number 1.1.1.95
    DNA
    TYPE functioning gene
    STRUCTURE 32.43 kb     12 Exon(s)
    Genomic sequence alignment details
    10 Kb 5' upstream gene genomic sequence study
    regulatory sequence Promoter (CAAT box)
    cytosine-phosphate-guanine/HTF
    Binding site   transcription factor
    text structure
  • positively regulated by the action of transcription factors Sp1 and NF-Y
  • promoter region exhibited several putative transcription factor binding sites for NF-Y, Sp1, GATA-1, TP53, AP2, and AP1, with no TATA-box motif
  • core positive promoter activity resided in the -276 to +1, which contains two GC-motifs for binding Sp1 and one CCAAT-motif for NF-Y.(both the proximal GC-motif and CCAAT-motif were crucial for full induction of the promoter activity)
    • MAPPING cloned Y linked N status provisional
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    12 splicing 2021 - 533 - 2000 10713460
    EXPRESSION
    Type widely
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestiveliver   highly Homo sapiens
    Lymphoid/Immunespleen   highly Homo sapiens
    Nervousbrain   highly Homo sapiens
    Reproductivemale systemtestis  highly Homo sapiens
    Urinarykidney   highly Homo sapiens
    cells
    SystemCellPubmedSpeciesStageRna symbol
    Nervousneuron Homo sapiens
    cell lineage
    cell lines
    fluid/secretion predominantly in lymph
    at STAGE
    physiological period fetal
    Text highly expressed in all fetal tissues, including brain tissue
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • each monomer comprises three distinct domains
  • a nucleotide-binding domain (residues 108–294)
  • a substrate-binding domain (residues 7–107 and 295–336)
  • a regulatory domain that binds serine (residues 337–533)
    • mono polymer homomer , tetramer
    HOMOLOGY
    interspecies homolog to rattus Phgdh (94.2 pc)
    homolog to murine Phdgh (94.6 pc)
    Homologene
    FAMILY
  • D-isomer specific 2-hydroxyacid dehydrogenase family
    • CATEGORY enzyme , transport carrier
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,cytoplasm,cytosolic,vesicle
    basic FUNCTION
  • involved in transition of phosphoglycerate to 3- phosphohydroxyglycerate, initiating and rate limiting step in the phosphorylated pathway of serine biosynthesis pathway
  • necessary for serine biosynthesis, which serves as a substrate for protein synthesis
  • catalyzes the first step in L-serine synthesis via the phosphorylated pathway
    • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS development , electron transport
    text
  • electron carrier
  • brain development
    • PATHWAY
    metabolism aminoacid
    signaling
    amino-acid biosynthesis (L-serine from 3-phospho-D-glyceric acid)
    a component
  • tetramer consisting of four identical subunits
    • INTERACTION
    DNA
    RNA
    small molecule cofactor, nucleotide,
  • NAD+
    • protein
  • target of HOXA10 regulation in endometrial cells
  • PRKCZ represses the expression of PHGDH and PSAT1, and phosphorylates PHGDH at key residues to inhibit its enzymatic activity
  • PRKCZ acts as a metabolic tumor suppressor by inhibiting PHGDH expression and activity
  • PHGDH promotes pancreatic cancer development through enhancing the translation initiations by interacting with EIF4A1 and EIF4E
    • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) PHGDH , NELAS
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    tumoral     --over  
    in leukemia, lymphoma and carcinoma
    constitutional     --other  
    in cycling endometrial tissue, is relatively high in the proliferative phase in glandular cells and lower in the secretory phase
    constitutional   deletion    
    L-serine deficiency caused by its deletion leads to robust induction of EIF4EBP1 and subsequent repression of translation initiation in the developing central nervous system
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS
  • impaired neurogenesis in embryonic spinal cord of Phgdh knockout mice, a serine deficiency disorder model
  • severe impairment in neurogenesis of the central nervous system of Phgdh knockout (KO) embryos and a reduction in the protein content of their brains