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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

PGD

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH.By similarity

Catalytic activityi

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH.

Pathwayi: pentose phosphate pathway

This protein is involved in step 3 of the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage).
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. Glucose-6-phosphate 1-dehydrogenase (zwf), Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase, Glucose-6-phosphate 1-dehydrogenase (zwf), Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase
  2. 6-phosphogluconolactonase (PGLS)
  3. 6-phosphogluconate dehydrogenase, decarboxylating, 6-phosphogluconate dehydrogenase, decarboxylating, 6-phosphogluconate dehydrogenase, decarboxylating (PGD), 6-phosphogluconate dehydrogenase, decarboxylating (gntZ)
This subpathway is part of the pathway pentose phosphate pathway, which is itself part of Carbohydrate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage), the pathway pentose phosphate pathway and in Carbohydrate degradation.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei103NADP1 Publication1
Binding sitei103SubstrateBy similarity1
Active sitei184Proton acceptorBy similarity1
Active sitei191Proton donorBy similarity1
Binding sitei192SubstrateBy similarity1
Binding sitei261Substrate; via amide nitrogenBy similarity1
Binding sitei288SubstrateBy similarity1
Binding sitei447Substrate; shared with dimeric partnerBy similarity1
Binding sitei453Substrate; shared with dimeric partnerBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 15NADP1 Publication6
Nucleotide bindingi33 – 35NADP1 Publication3
Nucleotide bindingi75 – 77NADP1 Publication3
Nucleotide bindingi478 – 481NADP; shared with dimeric partner1 Publication4

GO - Molecular functioni

GO - Biological processi

  • D-gluconate metabolic process Source: UniProtKB-KW
  • oxidation-reduction process Source: UniProtKB
  • pentose biosynthetic process Source: Ensembl
  • pentose-phosphate shunt Source: UniProtKB
  • pentose-phosphate shunt, oxidative branch Source: UniProtKB

Keywordsi

Molecular functionOxidoreductase
Biological processGluconate utilization, Pentose shunt
LigandNADP

Enzyme and pathway databases

BioCyciMetaCyc:HS06949-MONOMER
ReactomeiR-HSA-71336 Pentose phosphate pathway (hexose monophosphate shunt)
SABIO-RKiP52209
UniPathwayiUPA00115; UER00410

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:PGD
Synonyms:PGDH
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000142657.20
HGNCiHGNC:8891 PGD
MIMi172200 gene
neXtProtiNX_P52209

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

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

DisGeNETi5226
OpenTargetsiENSG00000142657
PharmGKBiPA33229

Chemistry databases

ChEMBLiCHEMBL3404
DrugBankiDB02076 6-Phosphogluconic Acid
DB00851 Dacarbazine
DB00695 Furosemide
DB00789 Gadopentetate dimeglumine
DB00920 Ketotifen
DB00814 Meloxicam
DB00563 Methotrexate
DB03962 Nicotinamide 8-Bromo-Adenine Dinucleotide Phosphate
DB00867 Ritodrine

Polymorphism and mutation databases

BioMutaiPGD
DMDMi20981679

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000900631 – 4836-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST483

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei38N6-acetyllysineBy similarity1
Modified residuei57PhosphoserineBy similarity1
Modified residuei59N6-acetyllysineCombined sources1
Modified residuei129PhosphoserineBy similarity1
Modified residuei309N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiP52209
MaxQBiP52209
PaxDbiP52209
PeptideAtlasiP52209
PRIDEiP52209
ProteomicsDBi56472
TopDownProteomicsiP52209-1 [P52209-1]

PTM databases

iPTMnetiP52209
PhosphoSitePlusiP52209
SwissPalmiP52209

Expressioni

Gene expression databases

BgeeiENSG00000142657
CleanExiHS_PGD
ExpressionAtlasiP52209 baseline and differential
GenevisibleiP52209 HS

Organism-specific databases

HPAiHPA031314
HPA031315

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi111247, 56 interactors
IntActiP52209, 20 interactors
MINTiP52209
STRINGi9606.ENSP00000270776

Chemistry databases

BindingDBiP52209

Structurei

Secondary structure

1483
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 9Combined sources6
Helixi13 – 24Combined sources12
Beta strandi29 – 32Combined sources4
Helixi37 – 44Combined sources8
Turni45 – 49Combined sources5
Helixi58 – 63Combined sources6
Beta strandi70 – 73Combined sources4
Helixi79 – 88Combined sources10
Helixi89 – 91Combined sources3
Beta strandi97 – 100Combined sources4
Helixi106 – 118Combined sources13
Beta strandi122 – 130Combined sources9
Helixi131 – 137Combined sources7
Beta strandi140 – 145Combined sources6
Helixi147 – 149Combined sources3
Helixi150 – 160Combined sources11
Turni165 – 167Combined sources3
Beta strandi169 – 171Combined sources3
Helixi179 – 207Combined sources29
Helixi213 – 223Combined sources11
Turni224 – 228Combined sources5
Helixi231 – 241Combined sources11
Beta strandi247 – 250Combined sources4
Helixi251 – 253Combined sources3
Helixi265 – 274Combined sources10
Helixi279 – 292Combined sources14
Helixi294 – 301Combined sources8
Helixi316 – 349Combined sources34
Helixi355 – 361Combined sources7
Helixi371 – 382Combined sources12
Helixi389 – 391Combined sources3
Helixi393 – 416Combined sources24
Helixi421 – 433Combined sources13
Helixi440 – 451Combined sources12
Beta strandi455 – 457Combined sources3
Beta strandi460 – 465Combined sources6

3D structure databases

ProteinModelPortaliP52209
SMRiP52209
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP52209

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni129 – 131Substrate bindingBy similarity3
Regioni187 – 188Substrate bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2653 Eukaryota
COG0362 LUCA
GeneTreeiENSGT00390000009023
HOGENOMiHOG000255147
HOVERGENiHBG000029
InParanoidiP52209
KOiK00033
OMAiNSHYPDS
OrthoDBiEOG091G06XF
PhylomeDBiP52209
TreeFamiTF300386

Family and domain databases

Gene3Di1.10.1040.10, 1 hit
InterProiView protein in InterPro
IPR008927 6-PGluconate_DH-like_C_sf
IPR013328 6PGD_dom2
IPR006114 6PGDH_C
IPR006113 6PGDH_Gnd/GntZ
IPR006115 6PGDH_NADP-bd
IPR006184 6PGdom_BS
IPR036291 NAD(P)-bd_dom_sf
IPR006183 Pgluconate_DH
PfamiView protein in Pfam
PF00393 6PGD, 1 hit
PF03446 NAD_binding_2, 1 hit
PIRSFiPIRSF000109 6PGD, 1 hit
PRINTSiPR00076 6PGDHDRGNASE
SMARTiView protein in SMART
SM01350 6PGD, 1 hit
SUPFAMiSSF48179 SSF48179, 1 hit
SSF51735 SSF51735, 1 hit
TIGRFAMsiTIGR00873 gnd, 1 hit
PROSITEiView protein in PROSITE
PS00461 6PGD, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P52209-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAQADIALIG LAVMGQNLIL NMNDHGFVVC AFNRTVSKVD DFLANEAKGT
60 70 80 90 100
KVVGAQSLKE MVSKLKKPRR IILLVKAGQA VDDFIEKLVP LLDTGDIIID
110 120 130 140 150
GGNSEYRDTT RRCRDLKAKG ILFVGSGVSG GEEGARYGPS LMPGGNKEAW
160 170 180 190 200
PHIKTIFQGI AAKVGTGEPC CDWVGDEGAG HFVKMVHNGI EYGDMQLICE
210 220 230 240 250
AYHLMKDVLG MAQDEMAQAF EDWNKTELDS FLIEITANIL KFQDTDGKHL
260 270 280 290 300
LPKIRDSAGQ KGTGKWTAIS ALEYGVPVTL IGEAVFARCL SSLKDERIQA
310 320 330 340 350
SKKLKGPQKF QFDGDKKSFL EDIRKALYAS KIISYAQGFM LLRQAATEFG
360 370 380 390 400
WTLNYGGIAL MWRGGCIIRS VFLGKIKDAF DRNPELQNLL LDDFFKSAVE
410 420 430 440 450
NCQDSWRRAV STGVQAGIPM PCFTTALSFY DGYRHEMLPA SLIQAQRDYF
460 470 480
GAHTYELLAK PGQFIHTNWT GHGGTVSSSS YNA
Length:483
Mass (Da):53,140
Last modified:January 23, 2007 - v3
Checksum:i6CEFC0077D1283E3
GO
Isoform 2 (identifier: P52209-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-13: Missing.

Note: No experimental confirmation available.
Show »
Length:470
Mass (Da):51,872
Checksum:i9099E0CF2995B8AD
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti118A → G in AAA75302 (PubMed:8978909).Curated1
Sequence conflicti135A → P in AAA75302 (PubMed:8978909).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_048104268A → S. Corresponds to variant dbSNP:rs11547610Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0557671 – 13Missing in isoform 2. 1 PublicationAdd BLAST13

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U30255 mRNA Translation: AAA75302.1
AK290404 mRNA Translation: BAF83093.1
AK298830 mRNA Translation: BAG60960.1
AL139424 Genomic DNA No translation available.
CH471130 Genomic DNA Translation: EAW71648.1
BC000368 mRNA Translation: AAH00368.1
CCDSiCCDS113.1 [P52209-1]
PIRiG01922
RefSeqiNP_001291380.1, NM_001304451.1
NP_001291381.1, NM_001304452.1 [P52209-2]
NP_002622.2, NM_002631.3 [P52209-1]
UniGeneiHs.464071

Genome annotation databases

EnsembliENST00000270776; ENSP00000270776; ENSG00000142657 [P52209-1]
GeneIDi5226
KEGGihsa:5226
UCSCiuc001arc.4 human [P52209-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry namei6PGD_HUMAN
AccessioniPrimary (citable) accession number: P52209
Secondary accession number(s): A8K2Y9, B4DQJ8, Q9BWD8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: July 18, 2018
This is version 182 of the entry and version 3 of the sequence. See complete history.
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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

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