PHGDH is human D-3-phosphoglycerate dehydrogenase (3-PGDH; EC 1.1.1.95), an NAD+-dependent oxidoreductase of the D-isomer-specific 2-hydroxyacid dehydrogenase family that assembles as a homotetramer and acts in the cytosol. It catalyzes the first and rate-limiting step of the phosphorylated pathway of de novo L-serine biosynthesis, oxidizing the glycolytic intermediate 3-phospho-D-glycerate to 3-phosphonooxypyruvate (3-phosphohydroxypyruvate) with reduction of NAD+ to NADH. Serine produced by this pathway supplies one-carbon units, nucleotides, glycine, phospholipids and redox cofactors. Human PHGDH additionally displays secondary NAD+-dependent 2-hydroxyacid dehydrogenase side-activities, most notably reduction of 2-oxoglutarate to the oncometabolite D-2-hydroxyglutarate, and in vitro malate dehydrogenase activity. Biallelic loss-of-function variants cause the serine-deficiency disorders phosphoglycerate dehydrogenase deficiency (congenital microcephaly, psychomotor retardation, seizures) and the more severe Neu-Laxova syndrome 1, while PHGDH amplification/overexpression drives serine biosynthesis in a subset of cancers. Two enzyme-independent moonlighting activities have additionally been reported in Alzheimer's-disease models: a nuclear, chromatin-associated transcriptional-regulator role acting through a predicted DNA-binding helix-helix-turn-helix subdomain, and, separately, an RNA-binding activity that binds the EIF2AK1 3'UTR and promotes BACE1 translation. Both are stated to be independent of catalysis, the second also independent of the first; both come from a single laboratory and neither has been independently replicated.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004617 phosphoglycerate dehydrogenase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Core molecular function. Phylogenetic (IBA) propagation of the phosphoglycerate dehydrogenase activity to human PHGDH is correct: this is the defining, physiologically dominant catalytic activity of the protein (EC 1.1.1.95), independently supported by direct human enzyme assays. Supporting Evidence: file:human/PHGDH/PHGDH-uniprot.txt Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- |
| GO:0004617 phosphoglycerate dehydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Same core molecular function reached electronically (RHEA:12641 / EC:1.1.1.95 mapping). Correct and redundant with the IBA and experimental support. Supporting Evidence: file:human/PHGDH/PHGDH-uniprot.txt Reaction=(2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH |
| GO:0006564 L-serine biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: Core biological process. PHGDH catalyzes step 1/3 of the L-serine biosynthesis pathway; InterPro2GO propagation is correct and corroborated by human experimental data (IMP, PMID:33758422). Supporting Evidence: file:human/PHGDH/PHGDH-uniprot.txt L-serine from |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Correct but a parent/grouping term: this is the general oxidoreductase class that subsumes the specific GO:0004617 phosphoglycerate dehydrogenase activity. Not wrong, but less informative than the specific MF, which is separately annotated. Keep as non-core (redundant generic ancestor). Supporting Evidence: file:human/PHGDH/PHGDH-uniprot.txt Reaction=(2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH |
| GO:0030060 L-malate dehydrogenase (NAD+) activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: Secondary in-vitro side-activity (EC 1.1.1.37), demonstrated biochemically for human PHGDH (PubMed:25406093) and captured by UniProt as an AltName. This is catalytic promiscuity of a 2-hydroxyacid dehydrogenase, not a described physiological role for PHGDH (malate oxidation is the job of the MDH enzymes). Not the core function; over-annotation if read as a genuine cellular malate dehydrogenase. Supporting Evidence: file:human/PHGDH/PHGDH-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | ACCEPT | Summary: Correct cofactor-binding molecular function. PHGDH is an NAD+-dependent dehydrogenase with a Rossmann-fold NAD(H)-binding domain and multiple crystallographically defined NAD+ binding sites. Retained as a supporting core molecular function. Supporting Evidence: file:human/PHGDH/PHGDH-uniprot.txt Reaction=(2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH |
| GO:0120568 (R)-2-hydroxyglutarate (NAD+) dehydrogenase activity | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Secondary moonlighting activity (EC 1.1.1.399), experimentally established for human PHGDH (PubMed:25406093, "Human phosphoglycerate dehydrogenase produces the oncometabolite D-2-hydroxyglutarate"). The GO term describes the reverse (2-HG oxidation) direction; PHGDH physiologically runs the reductive direction to make D-2-HG. Biologically real and relevant to oncometabolism, but not the core serine-biosynthesis function. Kept as non-core. Supporting Evidence: file:human/PHGDH/PHGDH-uniprot.txt Reaction=(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH + |
| GO:0005515 protein binding | IPI PMID:25036637 A quantitative chaperone interaction network reveals the arc... | REMOVE | Summary: Bare "protein binding" from a high-throughput chaperone/co-chaperone interaction network (LUMIER/AP-MS); WITH/FROM UniProtKB:Q9Y6I3 (EPN1). Uninformative for molecular function and not a characterized functional complex for PHGDH. Reason: No more informative molecular function is supportable from a high-throughput chaperone-network hit, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | REMOVE | Summary: Bare "protein binding" from the BioPlex 3.0 proteome-scale AP-MS interactome (WITH/FROM UniProtKB:Q9Y6I3, EPN1). High-throughput, uninformative for molecular function. Reason: No more informative molecular function is supportable from a proteome-scale AP-MS hit, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce... | REMOVE | Summary: Bare "protein binding" from the OpenCell endogenous-tagging interaction map (WITH/FROM UniProtKB:Q9Y6I3, EPN1). Same uninformative high-throughput interactor class. Reason: No more informative molecular function is supportable from an endogenous-tagging interaction map, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0004617 phosphoglycerate dehydrogenase activity | IMP PMID:33758422 Serine biosynthesis defect due to haploinsufficiency of PHGD... | ACCEPT | Summary: Direct experimental support for the core molecular function in human PHGDH. Eade et al. assayed enzymatic activity of PHGDH variants using 3-phosphoglycerate as substrate and NAD+ reduction as readout, showing that pathogenic missense variants reduce phosphoglycerate dehydrogenase activity (IMP by loss-of-function). Accept as a core-function annotation. Supporting Evidence: PMID:33758422 Enzyme activity was determined using 3-phosphoglycerate as a substrate and monitoring the reduction of the cofactor NAD+ to NADH |
| GO:0006564 L-serine biosynthetic process | IMP PMID:33758422 Serine biosynthesis defect due to haploinsufficiency of PHGD... | ACCEPT | Summary: Direct experimental support for the core biological process. A heterozygous loss-of-function PHGDH variant reduced 13C-glucose flux into serine/glycine and lowered cellular serine, demonstrating PHGDH's role in L-serine biosynthesis in human cells. Accept as a core-function annotation. Supporting Evidence: PMID:33758422 indicating decreased synthesis of serine/glycine via PHGDH |
| GO:0005829 cytosol | TAS Reactome:R-HSA-977348 | ACCEPT | Summary: Correct core subcellular localization. PHGDH is a soluble cytosolic enzyme catalyzing the first step of cytosolic serine biosynthesis; Reactome TAS is appropriate. |
| GO:0070062 extracellular exosome | HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres... | KEEP AS NON CORE | Summary: Detection of the abundant cytosolic enzyme PHGDH in extracellular exosome proteomics. A common non-specific finding for high-abundance metabolic enzymes and not indicative of a functional exosomal role. Keep as non-core. |
| GO:0070062 extracellular exosome | HDA PMID:19199708 Proteomic analysis of human parotid gland exosomes by multid... | KEEP AS NON CORE | Summary: Exosome proteomics detection (parotid gland exosomes). Non-specific high-throughput localization of an abundant cytosolic enzyme; not a core function. Keep as non-core. |
| GO:0070062 extracellular exosome | HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... | KEEP AS NON CORE | Summary: Exosome proteomics detection (urinary exosomes). Non-specific high-throughput localization; not a core function. Keep as non-core. |
| GO:0070062 extracellular exosome | HDA PMID:20458337 MHC class II-associated proteins in B-cell exosomes and pote... | KEEP AS NON CORE | Summary: Exosome proteomics detection (B-cell exosomes). Non-specific high-throughput localization of an abundant cytosolic enzyme; not a core function. Keep as non-core. |
| GO:0009055 electron transfer activity | TAS PMID:8758134 3-Phosphoglycerate dehydrogenase deficiency: an inborn error... | MARK AS OVER ANNOTATED | Summary: Incorrect molecular function. GO:0009055 electron transfer activity is for electron-carrier proteins of electron transport systems; PHGDH is a hydride-transferring NAD+-dependent dehydrogenase, not an electron carrier. The cited paper (Jaeken 1996) is a clinical description of 3-PGDH deficiency and does not support an electron transfer function. This is a legacy mis-mapping; over-annotation. |
| GO:0004617 phosphoglycerate dehydrogenase activity | TAS PMID:8758134 3-Phosphoglycerate dehydrogenase deficiency: an inborn error... | ACCEPT | Summary: Core molecular function, TAS from the original clinical/biochemical description of 3-PGDH deficiency, in which reduced phosphoglycerate dehydrogenase activity was demonstrated in patient fibroblasts. Consistent with the IBA/IEA/IMP support. Accept. Supporting Evidence: PMID:8758134 a decreased activity was demonstrated of 3-phosphoglycerate dehydrogenase |
| GO:0007420 brain development | TAS PMID:8758134 3-Phosphoglycerate dehydrogenase deficiency: an inborn error... | KEEP AS NON CORE | Summary: Downstream phenotypic consequence rather than a direct molecular role. Serine deficiency from 3-PGDH loss causes microcephaly and dysmyelination, reflecting serine's importance in the developing brain, but PHGDH's causal contribution is via serine biosynthesis, not a dedicated developmental function. Retain as non-core (pleiotropic/developmental). Supporting Evidence: PMID:8758134 congenital microcephaly, profound psychomotor retardation |
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Download this section (compressed HTML)Q: Can enzyme-independent nuclear/transcriptional and mRNA-binding activities of PHGDH be reproduced in an independent laboratory, at endogenous expression levels, in primary human astrocytes?
Suggested experts: Zhong S, Chen J
Q: If the two proposed moonlighting mechanisms are genuinely independent of each other, why does removing either one alone abolish the amyloid phenotype? Are they separable in the same experimental system?
Suggested experts: Zhong S
Q: Can a nucleic-acid-binding surface be demonstrated structurally within the PHGDH Rossmann fold without compromising NAD(H) binding, or does the predicted HHTH subdomain overlap the cofactor site?
Q: Is nuclear PHGDH a distinct pool with its own trafficking, or a minor redistribution of the abundant cytosolic enzyme detected under overexpression?
Suggested experts: Zhong S
Experiment: Determine a structure (or obtain quantitative EMSA/ITC binding constants) for recombinant PHGDH with the proposed target DNA, in the presence and absence of NAD+, and test whether the HHTH deletion that abolishes chromatin binding also perturbs cofactor binding or tetramer assembly - the obvious confound for a motif embedded in the Rossmann fold.
Hypothesis: PHGDH binds chromatin directly at IKKa (CHUK) and HMGB1 promoters through the predicted HHTH subdomain, independently of its catalytic cycle.
Type: structural biology / quantitative binding
Experiment: Use endogenously tagged PHGDH (knock-in, not transfection) in human iPSC-derived astrocytes with fractionation, proximity labelling and CUT&RUN/eCLIP, performed by a laboratory independent of the originating group, and compare against catalytically dead and HHTH-deleted knock-ins at native expression levels.
Hypothesis: Endogenous PHGDH is nuclear in human astrocytes and its non-catalytic activities are physiological rather than overexpression artefacts.
Type: endogenous tagging / independent replication
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: Whether PHGDH has any physiological non-enzymatic function is undetermined. Two enzyme-independent activities have been claimed - a nuclear DNA-binding transcriptional-regulator role and a sequence-specific mRNA 3'UTR-binding role - but they come from one laboratory, were published within a year of each other, and are asserted to be mutually independent rather than successive refinements of one mechanism. Neither has been replicated elsewhere, no structure of PHGDH bound to DNA or RNA has been reported, and the proposed nucleic-acid-binding surface lies inside the NAD(H)-binding Rossmann fold that carries the established catalytic function.
OPEN BIOLOGY
What is known: Firmly established and not in question: PHGDH is the NAD+-dependent 3-phosphoglycerate dehydrogenase (EC 1.1.1.95) catalysing the first, rate-limiting step of de novo L-serine biosynthesis in the cytosol, with human enzyme assays, loss-of-function disease genetics and flux measurements behind it. The moonlighting claims do not contest this and do not displace it.
Significance: A blood-brain-barrier-permeable inhibitor targeting the claimed transcriptional function has been proposed as an Alzheimer's therapeutic, so whether the non-catalytic activity is real determines whether that target exists. It also determines whether GO should ever carry nucleus, DNA-binding or mRNA-binding annotations for PHGDH, of which it currently has none.
What would resolve it: Independent replication outside the originating laboratory; endogenous (not overexpressed) nuclear PHGDH detection in human astrocytes by orthogonal methods; direct structural or quantitative binding evidence for PHGDH-DNA and PHGDH-RNA complexes; and a test of whether the two proposed mechanisms are separable in the same system, since each was reported to work without the other.
Provenance (the field's own admissions):
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