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Entry version 200 (13 Feb 2019)
Sequence version 4 (23 Jan 2007)
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Protein

D-3-phosphoglycerate dehydrogenase

Gene

PHGDH

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 4.5 min(-1) for 3-phosphoglycerate oxidation. kcat is 10.6 min(-1) for oxaloacetate reduction. kcat is 4.7 min(-1) for 2-oxoglutarate reduction.1 Publication
  1. KM=21.6 µM for 3-phosphonooxypyruvate1 Publication
  2. KM=0.26 mM for 3-phosphoglycerate1 Publication
  3. KM=6.5 mM for oxaloacetate1 Publication
  4. KM=10.1 mM for 2-oxoglutarate1 Publication
  5. KM=22 µM for NAD+1 Publication
  6. KM=4 µM for NADH1 Publication
  1. Vmax=35 nmol/min/mg enzyme with 3-phosphohydroxypyruvate as substrate (in patient-derived fibroblasts)1 Publication
  2. Vmax=168 nmol/min/mg enzyme with 3-phosphohydroxypyruvate as substrate (in 3-PGDH overexpressed cells)1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: L-serine biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes L-serine from 3-phospho-D-glycerate.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. D-3-phosphoglycerate dehydrogenase (HEL-S-113), D-3-phosphoglycerate dehydrogenase (PHGDH), D-3-phosphoglycerate dehydrogenase (PHGDH), D-3-phosphoglycerate dehydrogenase (PHGDH)
  2. Phosphoserine aminotransferase, Phosphoserine aminotransferase (PSAT1), Phosphoserine aminotransferase (PSAT1)
  3. Phosphoserine phosphatase (PSPH)
This subpathway is part of the pathway L-serine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-serine from 3-phospho-D-glycerate, the pathway L-serine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei78NAD1 Publication1
Binding sitei175NAD1 Publication1
Binding sitei207NAD; via carbonyl oxygen1 Publication1
<p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei2361
Binding sitei260NAD1 Publication1
Active sitei265By similarity1
Active sitei283Proton donor1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi155 – 156NAD1 Publication2
Nucleotide bindingi234 – 236NAD1 Publication3
Nucleotide bindingi283 – 286NAD1 Publication4

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • electron transfer activity Source: UniProtKB
  • L-malate dehydrogenase activity Source: UniProtKB-EC
  • NAD binding Source: InterPro
  • phosphoglycerate dehydrogenase activity Source: GO_Central

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionOxidoreductase
Biological processAmino-acid biosynthesis, Serine biosynthesis
LigandNAD

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

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BioCyci
MetaCyc:HS01776-MONOMER

BRENDA Comprehensive Enzyme Information System

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BRENDAi
1.1.1.95 2681

Reactome - a knowledgebase of biological pathways and processes

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Reactomei
R-HSA-977347 Serine biosynthesis

SIGNOR Signaling Network Open Resource

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SIGNORi
O43175

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00135;UER00196

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
D-3-phosphoglycerate dehydrogenase (EC:1.1.1.951 Publication)
Short name:
3-PGDH
Alternative name(s):
2-oxoglutarate reductaseCurated (EC:1.1.1.3991 Publication)
Malate dehydrogenaseCurated (EC:1.1.1.371 Publication)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:PHGDH
Synonyms:PGDH3
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiHomo sapiens (Human)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri9606 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000005640 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 1

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
HostDB:ENSG00000092621.11

Human Gene Nomenclature Database

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HGNCi
HGNC:8923 PHGDH

Online Mendelian Inheritance in Man (OMIM)

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MIMi
606879 gene

neXtProt; the human protein knowledge platform

More...
neXtProti
NX_O43175

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section provides information on the disease(s) associated with genetic variations in a given protein. The information is extracted from the scientific literature and diseases that are also described in the <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim">OMIM</a> database are represented with a <a href="http://www.uniprot.org/diseases">controlled vocabulary</a> in the following way:<p><a href='/help/involvement_in_disease' target='_top'>More...</a></p>Involvement in diseasei

Phosphoglycerate dehydrogenase deficiency (PHGDHD)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive inborn error of L-serine biosynthesis, clinically characterized by congenital microcephaly, psychomotor retardation, and seizures.
See also OMIM:601815
Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural variantiVAR_059026135R → W in PHGDHD; results in a 2-fold decrease in enzyme activity with 3-phosphohydroxypyruvate, but no change in substrate affinity. 1 PublicationCorresponds to variant dbSNP:rs267606949EnsemblClinVar.1
Natural variantiVAR_059027261V → M in PHGDHD; results in a four-fold decrease in substrate affinity and a slight increase in maximal enzyme activity with 3-phosphohydroxypyruvate. 1 PublicationCorresponds to variant dbSNP:rs267606947EnsemblClinVar.1
Natural variantiVAR_059028373A → T in PHGDHD; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate. 1 PublicationCorresponds to variant dbSNP:rs201553627Ensembl.1
Natural variantiVAR_059029377G → S in PHGDHD; results in a 2-fold decrease in enzyme activity with 3-phosphohydroxypyruvate, but no change in substrate affinity. 1 PublicationCorresponds to variant dbSNP:rs267606948EnsemblClinVar.1
Natural variantiVAR_013461425V → M in PHGDHD; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate. 2 PublicationsCorresponds to variant dbSNP:rs121907988EnsemblClinVar.1
Natural variantiVAR_059030490V → M in PHGDHD; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate. 3 PublicationsCorresponds to variant dbSNP:rs121907987EnsemblClinVar.1
Neu-Laxova syndrome 1 (NLS1)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA lethal, autosomal recessive multiple malformation syndrome characterized by ichthyosis, marked intrauterine growth restriction, microcephaly, short neck, limb deformities, hypoplastic lungs, edema, and central nervous system anomalies including lissencephaly, cerebellar hypoplasia and/or abnormal/agenesis of the corpus callosum. Abnormal facial features include severe proptosis with ectropion, hypertelorism, micrognathia, flattened nose, and malformed ears.
See also OMIM:256520
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_071819140G → R in NLS1. 1 PublicationCorresponds to variant dbSNP:rs587777770EnsemblClinVar.1
Natural variantiVAR_071820163R → Q in NLS1. 1 PublicationCorresponds to variant dbSNP:rs587777483EnsemblClinVar.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNET

More...
DisGeNETi
26227

MalaCards human disease database

More...
MalaCardsi
PHGDH
MIMi256520 phenotype
601815 phenotype

Open Targets

More...
OpenTargetsi
ENSG00000092621

Orphanet; a database dedicated to information on rare diseases and orphan drugs

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Orphaneti
79351 3-phosphoglycerate dehydrogenase deficiency, infantile/juvenile form
2671 Neu-Laxova syndrome

The Pharmacogenetics and Pharmacogenomics Knowledge Base

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PharmGKBi
PA33264

Chemistry databases

ChEMBL database of bioactive drug-like small molecules

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ChEMBLi
CHEMBL2311243

Drug and drug target database

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DrugBanki
DB00157 NADH

Polymorphism and mutation databases

BioMuta curated single-nucleotide variation and disease association database

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BioMutai
PHGDH

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved1 Publication
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000760122 – 533D-3-phosphoglycerate dehydrogenaseAdd BLAST532

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei2N-acetylalanine1 Publication1
Modified residuei14PhosphoserineCombined sources1
Modified residuei21N6-acetyllysine; alternateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>Cross-linki21Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateCombined sources
Cross-linki21Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei58N6-acetyllysineBy similarity1
Modified residuei78PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

Encyclopedia of Proteome Dynamics

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EPDi
O43175

jPOST - Japan Proteome Standard Repository/Database

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jPOSTi
O43175

MaxQB - The MaxQuant DataBase

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MaxQBi
O43175

PaxDb, a database of protein abundance averages across all three domains of life

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PaxDbi
O43175

PeptideAtlas

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PeptideAtlasi
O43175

PRoteomics IDEntifications database

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PRIDEi
O43175

ProteomicsDB human proteome resource

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ProteomicsDBi
48792

Consortium for Top Down Proteomics

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TopDownProteomicsi
O43175

PTM databases

CarbonylDB database of protein carbonylation sites

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CarbonylDBi
O43175

iPTMnet integrated resource for PTMs in systems biology context

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iPTMneti
O43175

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

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PhosphoSitePlusi
O43175

SwissPalm database of S-palmitoylation events

More...
SwissPalmi
O43175

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Induced by 17-beta-estradiol (estrogenic ligand) and 4-hydroxytamoxifen (agonist/antagonist ligand). Positively regulated by the transcription factors SP1 and NF-Y.2 Publications

Gene expression databases

Bgee dataBase for Gene Expression Evolution

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Bgeei
ENSG00000092621 Expressed in 222 organ(s), highest expression level in right lobe of liver

ExpressionAtlas, Differential and Baseline Expression

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ExpressionAtlasi
O43175 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

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Genevisiblei
O43175 HS

Organism-specific databases

Human Protein Atlas

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HPAi
CAB003681
CAB068216
HPA021241
HPA024031

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

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BioGridi
117618, 148 interactors

Protein interaction database and analysis system

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IntActi
O43175, 45 interactors

Molecular INTeraction database

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MINTi
O43175

STRING: functional protein association networks

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STRINGi
9606.ENSP00000358417

Chemistry databases

BindingDB database of measured binding affinities

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BindingDBi
O43175

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1533
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Select the link destinations:

Protein Data Bank Europe

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PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2G76X-ray1.70A/B4-315[»]
5N53X-ray1.48A/B100-294[»]
5N6CX-ray2.30A/B8-306[»]
5NZOX-ray1.29A/B100-294[»]
5NZPX-ray1.30A/B96-299[»]
5NZQX-ray1.50A/B93-315[»]
5OFMX-ray1.50A/B93-315[»]
5OFVX-ray1.50A/B93-315[»]
5OFWX-ray1.50A/B93-315[»]

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
O43175

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
O43175

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

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EvolutionaryTracei
O43175

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
KOG0068 Eukaryota
COG0111 LUCA

Ensembl GeneTree

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GeneTreei
ENSGT00940000155863

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

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HOGENOMi
HOG000136693

The HOVERGEN Database of Homologous Vertebrate Genes

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HOVERGENi
HBG054241

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
O43175

KEGG Orthology (KO)

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KOi
K00058

Identification of Orthologs from Complete Genome Data

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OMAi
NIAGMQV

Database of Orthologous Groups

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OrthoDBi
1537996at2759

Database for complete collections of gene phylogenies

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PhylomeDBi
O43175

TreeFam database of animal gene trees

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TreeFami
TF314548

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.30.1330.90, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR029009 ASB_dom_sf
IPR006139 D-isomer_2_OHA_DH_cat_dom
IPR029753 D-isomer_DH_CS
IPR029752 D-isomer_DH_CS1
IPR006140 D-isomer_DH_NAD-bd
IPR036291 NAD(P)-bd_dom_sf
IPR006236 PGDH

Pfam protein domain database

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Pfami
View protein in Pfam
PF00389 2-Hacid_dh, 1 hit
PF02826 2-Hacid_dh_C, 1 hit

Superfamily database of structural and functional annotation

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SUPFAMi
SSF143548 SSF143548, 1 hit
SSF51735 SSF51735, 1 hit

TIGRFAMs; a protein family database

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TIGRFAMsi
TIGR01327 PGDH, 1 hit

PROSITE; a protein domain and family database

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PROSITEi
View protein in PROSITE
PS00065 D_2_HYDROXYACID_DH_1, 1 hit
PS00670 D_2_HYDROXYACID_DH_2, 1 hit
PS00671 D_2_HYDROXYACID_DH_3, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequence (1+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 14 potential isoforms that are computationally mapped.Show allAlign All

O43175-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAFANLRKVL ISDSLDPCCR KILQDGGLQV VEKQNLSKEE LIAELQDCEG
60 70 80 90 100
LIVRSATKVT ADVINAAEKL QVVGRAGTGV DNVDLEAATR KGILVMNTPN
110 120 130 140 150
GNSLSAAELT CGMIMCLARQ IPQATASMKD GKWERKKFMG TELNGKTLGI
160 170 180 190 200
LGLGRIGREV ATRMQSFGMK TIGYDPIISP EVSASFGVQQ LPLEEIWPLC
210 220 230 240 250
DFITVHTPLL PSTTGLLNDN TFAQCKKGVR VVNCARGGIV DEGALLRALQ
260 270 280 290 300
SGQCAGAALD VFTEEPPRDR ALVDHENVIS CPHLGASTKE AQSRCGEEIA
310 320 330 340 350
VQFVDMVKGK SLTGVVNAQA LTSAFSPHTK PWIGLAEALG TLMRAWAGSP
360 370 380 390 400
KGTIQVITQG TSLKNAGNCL SPAVIVGLLK EASKQADVNL VNAKLLVKEA
410 420 430 440 450
GLNVTTSHSP AAPGEQGFGE CLLAVALAGA PYQAVGLVQG TTPVLQGLNG
460 470 480 490 500
AVFRPEVPLR RDLPLLLFRT QTSDPAMLPT MIGLLAEAGV RLLSYQTSLV
510 520 530
SDGETWHVMG ISSLLPSLEA WKQHVTEAFQ FHF
Length:533
Mass (Da):56,651
Last modified:January 23, 2007 - v4
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iC58EB72275C45B35
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There are 14 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A286YF22A0A286YF22_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
526Annotation score:

Annotation score:2 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A2C9F2M7A0A2C9F2M7_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
532Annotation score:

Annotation score:2 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A286YFM8A0A286YFM8_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
239Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A286YF78A0A286YF78_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
276Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A286YFA2A0A286YFA2_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
445Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A286YFL2A0A286YFL2_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
429Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A286YFE1A0A286YFE1_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
89Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A286YER3A0A286YER3_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
97Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A286YFC8A0A286YFC8_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
123Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
A0A286YF34A0A286YF34_HUMAN
D-3-phosphoglycerate dehydrogenase
PHGDH
72Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
There are more potential isoformsShow all

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti25D → E in AAB88664 (PubMed:10713460).Curated1
Sequence conflicti25D → E in AAD51415 (PubMed:10713460).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_059026135R → W in PHGDHD; results in a 2-fold decrease in enzyme activity with 3-phosphohydroxypyruvate, but no change in substrate affinity. 1 PublicationCorresponds to variant dbSNP:rs267606949EnsemblClinVar.1
Natural variantiVAR_071819140G → R in NLS1. 1 PublicationCorresponds to variant dbSNP:rs587777770EnsemblClinVar.1
Natural variantiVAR_071820163R → Q in NLS1. 1 PublicationCorresponds to variant dbSNP:rs587777483EnsemblClinVar.1
Natural variantiVAR_059027261V → M in PHGDHD; results in a four-fold decrease in substrate affinity and a slight increase in maximal enzyme activity with 3-phosphohydroxypyruvate. 1 PublicationCorresponds to variant dbSNP:rs267606947EnsemblClinVar.1
Natural variantiVAR_059028373A → T in PHGDHD; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate. 1 PublicationCorresponds to variant dbSNP:rs201553627Ensembl.1
Natural variantiVAR_059029377G → S in PHGDHD; results in a 2-fold decrease in enzyme activity with 3-phosphohydroxypyruvate, but no change in substrate affinity. 1 PublicationCorresponds to variant dbSNP:rs267606948EnsemblClinVar.1
Natural variantiVAR_013461425V → M in PHGDHD; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate. 2 PublicationsCorresponds to variant dbSNP:rs121907988EnsemblClinVar.1
Natural variantiVAR_059030490V → M in PHGDHD; results in almost undetectable enzyme activity with 3-phosphohydroxypyruvate. 3 PublicationsCorresponds to variant dbSNP:rs121907987EnsemblClinVar.1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AF006043 mRNA Translation: AAB88664.1
AF171237 mRNA Translation: AAD51415.1
CR456795 mRNA Translation: CAG33076.1
AK315360 mRNA Translation: BAG37755.1
AL589734 Genomic DNA No translation available.
AL139251 Genomic DNA No translation available.
CH471122 Genomic DNA Translation: EAW56708.1
BC000303 mRNA Translation: AAH00303.1
BC001349 mRNA Translation: AAH01349.1
BC011262 mRNA Translation: AAH11262.1

The Consensus CDS (CCDS) project

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CCDSi
CCDS904.1

NCBI Reference Sequences

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RefSeqi
NP_006614.2, NM_006623.3

UniGene gene-oriented nucleotide sequence clusters

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UniGenei
Hs.487296

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENST00000641023; ENSP00000493175; ENSG00000092621
ENST00000641597; ENSP00000493382; ENSG00000092621

Database of genes from NCBI RefSeq genomes

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GeneIDi
26227

KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGGi
hsa:26227

UCSC genome browser

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UCSCi
uc001ehz.4 human

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF006043 mRNA Translation: AAB88664.1
AF171237 mRNA Translation: AAD51415.1
CR456795 mRNA Translation: CAG33076.1
AK315360 mRNA Translation: BAG37755.1
AL589734 Genomic DNA No translation available.
AL139251 Genomic DNA No translation available.
CH471122 Genomic DNA Translation: EAW56708.1
BC000303 mRNA Translation: AAH00303.1
BC001349 mRNA Translation: AAH01349.1
BC011262 mRNA Translation: AAH11262.1
CCDSiCCDS904.1
RefSeqiNP_006614.2, NM_006623.3
UniGeneiHs.487296

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2G76X-ray1.70A/B4-315[»]
5N53X-ray1.48A/B100-294[»]
5N6CX-ray2.30A/B8-306[»]
5NZOX-ray1.29A/B100-294[»]
5NZPX-ray1.30A/B96-299[»]
5NZQX-ray1.50A/B93-315[»]
5OFMX-ray1.50A/B93-315[»]
5OFVX-ray1.50A/B93-315[»]
5OFWX-ray1.50A/B93-315[»]
ProteinModelPortaliO43175
SMRiO43175
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117618, 148 interactors
IntActiO43175, 45 interactors
MINTiO43175
STRINGi9606.ENSP00000358417

Chemistry databases

BindingDBiO43175
ChEMBLiCHEMBL2311243
DrugBankiDB00157 NADH

PTM databases

CarbonylDBiO43175
iPTMnetiO43175
PhosphoSitePlusiO43175
SwissPalmiO43175

Polymorphism and mutation databases

BioMutaiPHGDH

Proteomic databases

EPDiO43175
jPOSTiO43175
MaxQBiO43175
PaxDbiO43175
PeptideAtlasiO43175
PRIDEiO43175
ProteomicsDBi48792
TopDownProteomicsiO43175

Protocols and materials databases

The DNASU plasmid repository

More...
DNASUi
26227
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000641023; ENSP00000493175; ENSG00000092621
ENST00000641597; ENSP00000493382; ENSG00000092621
GeneIDi26227
KEGGihsa:26227
UCSCiuc001ehz.4 human

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
26227
DisGeNETi26227
EuPathDBiHostDB:ENSG00000092621.11

GeneCards: human genes, protein and diseases

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GeneCardsi
PHGDH
HGNCiHGNC:8923 PHGDH
HPAiCAB003681
CAB068216
HPA021241
HPA024031
MalaCardsiPHGDH
MIMi256520 phenotype
601815 phenotype
606879 gene
neXtProtiNX_O43175
OpenTargetsiENSG00000092621
Orphaneti79351 3-phosphoglycerate dehydrogenase deficiency, infantile/juvenile form
2671 Neu-Laxova syndrome
PharmGKBiPA33264

GenAtlas: human gene database

More...
GenAtlasi
Search...

Phylogenomic databases

eggNOGiKOG0068 Eukaryota
COG0111 LUCA
GeneTreeiENSGT00940000155863
HOGENOMiHOG000136693
HOVERGENiHBG054241
InParanoidiO43175
KOiK00058
OMAiNIAGMQV
OrthoDBi1537996at2759
PhylomeDBiO43175
TreeFamiTF314548

Enzyme and pathway databases

UniPathwayi
UPA00135;UER00196

BioCyciMetaCyc:HS01776-MONOMER
BRENDAi1.1.1.95 2681
ReactomeiR-HSA-977347 Serine biosynthesis
SIGNORiO43175

Miscellaneous databases

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

More...
ChiTaRSi
PHGDH human
EvolutionaryTraceiO43175

The Gene Wiki collection of pages on human genes and proteins

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GeneWikii
Phosphoglycerate_dehydrogenase

Database of phenotypes from RNA interference screens in Drosophila and Homo sapiens

More...
GenomeRNAii
26227

Protein Ontology

More...
PROi
PR:O43175

The Stanford Online Universal Resource for Clones and ESTs

More...
SOURCEi
Search...

Gene expression databases

BgeeiENSG00000092621 Expressed in 222 organ(s), highest expression level in right lobe of liver
ExpressionAtlasiO43175 baseline and differential
GenevisibleiO43175 HS

Family and domain databases

Gene3Di3.30.1330.90, 1 hit
InterProiView protein in InterPro
IPR029009 ASB_dom_sf
IPR006139 D-isomer_2_OHA_DH_cat_dom
IPR029753 D-isomer_DH_CS
IPR029752 D-isomer_DH_CS1
IPR006140 D-isomer_DH_NAD-bd
IPR036291 NAD(P)-bd_dom_sf
IPR006236 PGDH
PfamiView protein in Pfam
PF00389 2-Hacid_dh, 1 hit
PF02826 2-Hacid_dh_C, 1 hit
SUPFAMiSSF143548 SSF143548, 1 hit
SSF51735 SSF51735, 1 hit
TIGRFAMsiTIGR01327 PGDH, 1 hit
PROSITEiView protein in PROSITE
PS00065 D_2_HYDROXYACID_DH_1, 1 hit
PS00670 D_2_HYDROXYACID_DH_2, 1 hit
PS00671 D_2_HYDROXYACID_DH_3, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiSERA_HUMAN
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: O43175
Secondary accession number(s): B2RD08, Q5SZU3, Q9BQ01
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: January 23, 2007
Last modified: February 13, 2019
This is version 200 of the entry and version 4 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  5. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  6. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  7. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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