Human Gene PGD (ENST00000270776.13_4) from GENCODE V47lift37
  Description: phosphogluconate dehydrogenase, transcript variant 1 (from RefSeq NM_002631.4)
Gencode Transcript: ENST00000270776.13_4
Gencode Gene: ENSG00000142657.21_10
Transcript (Including UTRs)
   Position: hg19 chr1:10,459,121-10,480,568 Size: 21,448 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr1:10,459,175-10,479,806 Size: 20,632 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:10,459,121-10,480,568)mRNA (may differ from genome)Protein (483 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: 6PGD_HUMAN
DESCRIPTION: RecName: Full=6-phosphogluconate dehydrogenase, decarboxylating; EC=1.1.1.44;
FUNCTION: Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH (By similarity).
CATALYTIC ACTIVITY: 6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH.
PATHWAY: Carbohydrate degradation; pentose phosphate pathway; D- ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 3/3.
SUBUNIT: Homodimer.
INTERACTION: O95777:NAA38; NbExp=1; IntAct=EBI-372761, EBI-347779;
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
SIMILARITY: Belongs to the 6-phosphogluconate dehydrogenase family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PGD
Diseases sorted by gene-association score: cutaneous leishmaniasis (19), 6-phosphogluconate dehydrogenase deficiency (13), visceral leishmaniasis (11), glucosephosphate dehydrogenase deficiency (9), sleeping sickness (7)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 304.58 RPKM in Whole Blood
Total median expression: 1964.90 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -6.1054-0.113 Picture PostScript Text
3' UTR -207.20762-0.272 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008927 - 6-PGluconate_DH_C-like
IPR006114 - 6PGDH_C
IPR006113 - 6PGDH_decarbox
IPR006115 - 6PGDH_NADP-bd
IPR006184 - 6PGdom_BS
IPR013328 - DH_multihelical
IPR012284 - Fibritin/6PGD_C-extension
IPR016040 - NAD(P)-bd_dom

Pfam Domains:
PF00393 - 6-phosphogluconate dehydrogenase, C-terminal domain
PF03446 - NAD binding domain of 6-phosphogluconate dehydrogenase

SCOP Domains:
48179 - 6-phosphogluconate dehydrogenase C-terminal domain-like
51735 - NAD(P)-binding Rossmann-fold domains
51984 - MurCD N-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2JKV - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P52209
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004616 phosphogluconate dehydrogenase (decarboxylating) activity
GO:0016491 oxidoreductase activity

Biological Process:
GO:0006098 pentose-phosphate shunt
GO:0009051 pentose-phosphate shunt, oxidative branch
GO:0019322 pentose biosynthetic process
GO:0019521 D-gluconate metabolic process
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF383928 - JP 2014500723-A/191431: Polycomb-Associated Non-Coding RNAs.
AK300952 - Homo sapiens cDNA FLJ52522 complete cds, highly similar to 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44).
AK304423 - Homo sapiens cDNA FLJ53132 complete cds, highly similar to 6-phosphogluconate dehydrogenase,decarboxylating (EC 1.1.1.44).
AK303898 - Homo sapiens cDNA FLJ51182 complete cds, highly similar to 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44).
AK290404 - Homo sapiens cDNA FLJ75631 complete cds, highly similar to Homo sapiens phosphogluconate dehydrogenase (PGD), mRNA.
AK296889 - Homo sapiens cDNA FLJ52439 complete cds, highly similar to 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44).
BC000368 - Homo sapiens phosphogluconate dehydrogenase, mRNA (cDNA clone MGC:8331 IMAGE:2819330), complete cds.
LF357416 - JP 2014500723-A/164919: Polycomb-Associated Non-Coding RNAs.
U30255 - Homo sapiens phosphogluconate dehydrogenase (PGDH) mRNA, complete cds.
AB463169 - Synthetic construct DNA, clone: pF1KB5457, Homo sapiens PGD gene for phosphogluconate dehydrogenase, without stop codon, in Flexi system.
AK298830 - Homo sapiens cDNA FLJ52518 complete cds, highly similar to 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44).
LP747432 - Sequence 19 from Patent WO2018009939.
CU674180 - Synthetic construct Homo sapiens gateway clone IMAGE:100017675 5' read PGD mRNA.
KJ891789 - Synthetic construct Homo sapiens clone ccsbBroadEn_01183 PGD gene, encodes complete protein.
LF357415 - JP 2014500723-A/164918: Polycomb-Associated Non-Coding RNAs.
LF357412 - JP 2014500723-A/164915: Polycomb-Associated Non-Coding RNAs.
LF357411 - JP 2014500723-A/164914: Polycomb-Associated Non-Coding RNAs.
LF357409 - JP 2014500723-A/164912: Polycomb-Associated Non-Coding RNAs.
LF357408 - JP 2014500723-A/164911: Polycomb-Associated Non-Coding RNAs.
LF357406 - JP 2014500723-A/164909: Polycomb-Associated Non-Coding RNAs.
LF357404 - JP 2014500723-A/164907: Polycomb-Associated Non-Coding RNAs.
LF357402 - JP 2014500723-A/164905: Polycomb-Associated Non-Coding RNAs.
LF357401 - JP 2014500723-A/164904: Polycomb-Associated Non-Coding RNAs.
LF357400 - JP 2014500723-A/164903: Polycomb-Associated Non-Coding RNAs.
LF357399 - JP 2014500723-A/164902: Polycomb-Associated Non-Coding RNAs.
LF357398 - JP 2014500723-A/164901: Polycomb-Associated Non-Coding RNAs.
JD316753 - Sequence 297777 from Patent EP1572962.
JD230603 - Sequence 211627 from Patent EP1572962.
LF357397 - JP 2014500723-A/164900: Polycomb-Associated Non-Coding RNAs.
MA619505 - JP 2018138019-A/191431: Polycomb-Associated Non-Coding RNAs.
MA592993 - JP 2018138019-A/164919: Polycomb-Associated Non-Coding RNAs.
MA592992 - JP 2018138019-A/164918: Polycomb-Associated Non-Coding RNAs.
MA592989 - JP 2018138019-A/164915: Polycomb-Associated Non-Coding RNAs.
MA592988 - JP 2018138019-A/164914: Polycomb-Associated Non-Coding RNAs.
MA592986 - JP 2018138019-A/164912: Polycomb-Associated Non-Coding RNAs.
MA592985 - JP 2018138019-A/164911: Polycomb-Associated Non-Coding RNAs.
MA592983 - JP 2018138019-A/164909: Polycomb-Associated Non-Coding RNAs.
MA592981 - JP 2018138019-A/164907: Polycomb-Associated Non-Coding RNAs.
MA592979 - JP 2018138019-A/164905: Polycomb-Associated Non-Coding RNAs.
MA592978 - JP 2018138019-A/164904: Polycomb-Associated Non-Coding RNAs.
MA592977 - JP 2018138019-A/164903: Polycomb-Associated Non-Coding RNAs.
MA592976 - JP 2018138019-A/164902: Polycomb-Associated Non-Coding RNAs.
MA592975 - JP 2018138019-A/164901: Polycomb-Associated Non-Coding RNAs.
MA592974 - JP 2018138019-A/164900: Polycomb-Associated Non-Coding RNAs.
MB486572 - JP 2019531699-A/19: METHODS FOR DIAGNOSING AND TREATING CANCER.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
OXIDATIVEPENT-PWY - pentose phosphate pathway (oxidative branch)

Reactome (by CSHL, EBI, and GO)

Protein P52209 (Reactome details) participates in the following event(s):

R-HSA-71299 6-phospho-D-gluconate + NADP+ => D-ribulose 5-phosphate + CO2 + NADPH + H+
R-HSA-71336 Pentose phosphate pathway (hexose monophosphate shunt)
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: 6PGD_HUMAN, A8K2Y9, B4DQJ8, ENST00000270776.1, ENST00000270776.10, ENST00000270776.11, ENST00000270776.12, ENST00000270776.2, ENST00000270776.3, ENST00000270776.4, ENST00000270776.5, ENST00000270776.6, ENST00000270776.7, ENST00000270776.8, ENST00000270776.9, NM_002631, P52209, PGDH, Q9BWD8, uc317ivd.1, uc317ivd.2
UCSC ID: ENST00000270776.13_4
RefSeq Accession: NM_002631.4
Protein: P52209 (aka 6PGD_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.