PGD phosphogluconate dehydrogenase [Homo sapiens (human)] - Gene

Summary

Go to the top of the page Help

Official Symbol: PGDprovided by HGNC
Official Full Name: phosphogluconate dehydrogenaseprovided by HGNC
Primary source: HGNC:8891
See related: Ensembl:ENSG00000142657; HPRD:01391; MIM:172200; Vega:OTTHUMG00000001905
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: 6PGD
Summary: 6-phosphogluconate dehydrogenase is the second dehydrogenase in the pentose phosphate shunt. Deficiency of this enzyme is generally asymptomatic, and the inheritance of this disorder is autosomal dominant. Hemolysis results from combined deficiency of 6-phosphogluconate dehydrogenase and 6-phosphogluconolactonase suggesting a synergism of the two enzymopathies. [provided by RefSeq, Jul 2008]

Genomic context

Go to the top of the page Help

Location :: 1p36.22

Sequence :: Chromosome: 1; NC_000001.10 (10459085..10480201)

See PGD in Epigenomics, MapViewer

Chromosome 1 - NC_000001.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions What's a GeneRIF?

Glycolytic cancer cells lacking 6-phosphogluconate dehydrogenase metabolize glucose to induce senescence
Title: Glycolytic cancer cells lacking 6-phosphogluconate dehydrogenase metabolize glucose to induce senescence.
A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration.
Title: Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration.
Data suggest that the affinity of Nox2 for NADPH is increased in the presence of 6PGDH on cell stimulation.
Title: Coupling of 6-phosphogluconate dehydrogenase with NADPH oxidase in neutrophils: Nox2 activity regulation by NADPH availability.
Hsa-miR-132 and -212 were negatively correlated with PGD in the prefrontal cortex of individuals affected with schizophrenia and bipolar disorders.
Title: MicroRNA expression profiling in the prefrontal cortex of individuals affected with schizophrenia and bipolar disorders.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

NHGRI GWAS Catalog

Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers.

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Source	Pubs	Description
P52209	Q04446	GBE1	HPRD	PubMed
P52209	O95777	NAA38	HPRD	PubMed
BioGRID:111247	BioGRID:115846	AHSA1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:106990	ALDH7A1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:106725	ALDH9A1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:121897	C12orf10	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:107452	CDK2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:107454	CDK4	BioGRID	PubMed	Two-hybrid
BioGRID:111247	BioGRID:117929	CHORDC1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:108258	EEF2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:113297	EIF4H	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:108814	G6PD	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:108981	GLA	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:109035	GNAI3	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:109391	HMGB2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:115015	IQCB1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:114995	ISG15	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:110131	LDHA	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:110137	LDHB	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:119679	NAA38	BioGRID	PubMed	Two-hybrid
BioGRID:111247	BioGRID:115669	NDRG1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:109180	PDIA3	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:112109	RPS6KA1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:112535	SORD	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:112497	SUMO2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:112779	TCEA1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:112872	TERF1	BioGRID	PubMed	Two-hybrid
BioGRID:111247	BioGRID:112910	TGM2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:112921	THOP1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:123529	TXNDC5	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:115503	USPL1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:113361	YWHAB	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:113364	YWHAG	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111247	BioGRID:116168	YWHAQ	BioGRID	PubMed	Affinity Capture-MS

Pathways from BioSystems

Go to the top of the page Help

Glutathione metabolism, organism-specific biosystem (from KEGG)
Glutathione metabolism, organism-specific biosystem
Glutathione metabolism
Glutathione metabolism, conserved biosystem (from KEGG)
Glutathione metabolism, conserved biosystem
Glutathione metabolism
Metabolism, organism-specific biosystem (from REACTOME)
Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
Metabolism of carbohydrates, organism-specific biosystem (from REACTOME)
Metabolism of carbohydrates, organism-specific biosystemThese pathways together are responsible for: 1) the extraction of energy and carbon skeletons for biosyntheses from dietary sugars and related molecules; 2) the short-term storage of glucose in the b...
Pentose Phosphate Pathway, organism-specific biosystem (from WikiPathways)
Pentose Phosphate Pathway, organism-specific biosystem
Pentose Phosphate Pathway
Pentose phosphate pathway, organism-specific biosystem (from KEGG)
Pentose phosphate pathway, organism-specific biosystemThe pentose phosphate pathway is a process of glucose turnover that produces NADPH as reducing equivalents and pentoses as essential parts of nucleotides. There are two different phases in the pathwa...
Pentose phosphate pathway, conserved biosystem (from KEGG)
Pentose phosphate pathway, conserved biosystemThe pentose phosphate pathway is a process of glucose turnover that produces NADPH as reducing equivalents and pentoses as essential parts of nucleotides. There are two different phases in the pathwa...
Pentose phosphate pathway (Pentose phosphate cycle), organism-specific biosystem (from KEGG)
Pentose phosphate pathway (Pentose phosphate cycle), organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
Pentose phosphate pathway (Pentose phosphate cycle), conserved biosystem (from KEGG)
Pentose phosphate pathway (Pentose phosphate cycle), conserved biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
Pentose phosphate pathway (hexose monophosphate shunt), organism-specific biosystem (from REACTOME)
Pentose phosphate pathway (hexose monophosphate shunt), organism-specific biosystemThe pentose phosphate pathway is responsible for the generation of a substantial fraction of the cytoplasmic NADPH required for biosynthetic reactions, and for the generation of ribose 5-phosphate fo...
Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P, organism-specific biosystem (from KEGG)
Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P, organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P, conserved biosystem (from KEGG)
Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P, conserved biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
pentose phosphate pathway, organism-specific biosystem (from BIOCYC)
pentose phosphate pathway, organism-specific biosystem
pentose phosphate pathway
pentose phosphate pathway (oxidative branch), organism-specific biosystem (from BIOCYC)
pentose phosphate pathway (oxidative branch), organism-specific biosystem
pentose phosphate pathway (oxidative branch)

General gene information

Go to the top of the page Help

Markers

PGD (e-PCR), detects polymorphism
- UniSTS:503297

RH66785 (e-PCR)
- UniSTS:9752

RH39270 (e-PCR)
- UniSTS:85323

RH70785 (e-PCR)
- UniSTS:32368

SHGC-105729 (e-PCR)
- UniSTS:169387

SHGC-74199 (e-PCR)
- UniSTS:78280

Homology

Homologs of the PGD gene: The PGD gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, and N.crassa.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
NADP binding	IEA Inferred from Electronic Annotation more info
phosphogluconate dehydrogenase (decarboxylating) activity	EXP Inferred from Experiment more info
phosphogluconate dehydrogenase (decarboxylating) activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
D-gluconate metabolic process	IEA Inferred from Electronic Annotation more info
carbohydrate metabolic process	TAS Traceable Author Statement more info
oxidation-reduction process	IDA Inferred from Direct Assay more info	PubMed
pentose biosynthetic process	IEA Inferred from Electronic Annotation more info
pentose-phosphate shunt	ISS Inferred from Sequence or Structural Similarity more info
pentose-phosphate shunt	TAS Traceable Author Statement more info
pentose-phosphate shunt, oxidative branch	IDA Inferred from Direct Assay more info	PubMed
small molecule metabolic process	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
cytosol	TAS Traceable Author Statement more info

General protein information

Go to the top of the page Help

Preferred Names: 6-phosphogluconate dehydrogenase, decarboxylating

Names: 6-phosphogluconate dehydrogenase, decarboxylating

NP_002622.2

EC 1.1.1.44

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_002631.2 → NP_002622.2 6-phosphogluconate dehydrogenase, decarboxylating

Status: REVIEWED

Source sequence(s)

BC000368, CD700605

Consensus CDS

CCDS113.1

UniProtKB/Swiss-Prot

P52209

Related

ENSP00000270776, OTTHUMP00000001897, ENST00000270776, OTTHUMT00000005398

Conserved Domains (3) summary

pfam00393
Location:180 – 470
Blast Score: 1476

6PGD; 6-phosphogluconate dehydrogenase, C-terminal domain

PRK09287
Location:14 – 473
Blast Score: 2138

PRK09287; 6-phosphogluconate dehydrogenase; Validated

cl09931
Location:5 – 288
Blast Score: 614

NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000001.10 Reference GRCh37.p10 Primary Assembly

Range

10459085..10480201

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000133.1 Alternate HuRef

Range

9612776..9633839

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018912.1 Alternate CHM1_1.0

Range

10477259..10498376

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01035601.1 (2465..9000)	None
genomic	ABBA01035602.1	None
genomic	ABBA01035603.1	None
genomic	AL139424.21 (44056..65172)	None
genomic	AMYH01000246.1 (66519..87636)	None
genomic	CH471130.1	EAW71647.1
		EAW71648.1
mRNA	AK290404.1	BAF83093.1
mRNA	AK296889.1	BAG59448.1
mRNA	AK298830.1	BAG60960.1
mRNA	AK300952.1	BAG62580.1
mRNA	AK303898.1	BAG64830.1
mRNA	AK304423.1	BAG65252.1
mRNA	BC000368.2	AAH00368.1
mRNA	CD700605.1	None
mRNA	U30255.1	AAA75302.1