Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

PGD

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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 (G6PD), Glucose-6-phosphate 1-dehydrogenase, 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)
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
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

BioCyciMetaCyc:HS06949-MONOMER.
ZFISH:HS06949-MONOMER.
ReactomeiR-HSA-71336. Pentose phosphate pathway (hexose monophosphate shunt).
SABIO-RKP52209.
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

HGNCiHGNC:8891. PGD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • extracellular exosome Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

DisGeNETi5226.
OpenTargetsiENSG00000142657.
PharmGKBiPA33229.

Chemistry databases

ChEMBLiCHEMBL3404.
DrugBankiDB00851. Dacarbazine.
DB00695. Furosemide.
DB00789. Gadopentetate dimeglumine.
DB00920. Ketotifen.
DB00814. Meloxicam.
DB00563. Methotrexate.
DB00867. Ritodrine.

Polymorphism and mutation databases

BioMutaiPGD.
DMDMi20981679.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000900632 – 4836-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST482

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.
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. 54 interactors.
IntActiP52209. 11 interactors.
MINTiMINT-1415782.
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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JKVX-ray2.53A/B/C/D/E/F1-483[»]
4GWGX-ray1.39A2-483[»]
4GWKX-ray1.53A2-483[»]
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.
OMAiEPCVAYL.
OrthoDBiEOG091G06XF.
PhylomeDBiP52209.
TreeFamiTF300386.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR012284. 6PGD_dom_3.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_Gnd/GntZ.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR016040. NAD(P)-bd_dom.
IPR006183. Pgluconate_DH.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
PRINTSiPR00076. 6PGDHDRGNASE.
SMARTiSM01350. 6PGD. 1 hit.
[Graphical view]
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

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 rs11547610dbSNPEnsembl.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. Translation: CAI95751.1.
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

Cross-referencesi

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. Translation: CAI95751.1.
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JKVX-ray2.53A/B/C/D/E/F1-483[»]
4GWGX-ray1.39A2-483[»]
4GWKX-ray1.53A2-483[»]
ProteinModelPortaliP52209.
SMRiP52209.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111247. 54 interactors.
IntActiP52209. 11 interactors.
MINTiMINT-1415782.
STRINGi9606.ENSP00000270776.

Chemistry databases

BindingDBiP52209.
ChEMBLiCHEMBL3404.
DrugBankiDB00851. Dacarbazine.
DB00695. Furosemide.
DB00789. Gadopentetate dimeglumine.
DB00920. Ketotifen.
DB00814. Meloxicam.
DB00563. Methotrexate.
DB00867. Ritodrine.

PTM databases

iPTMnetiP52209.
PhosphoSitePlusiP52209.
SwissPalmiP52209.

Polymorphism and mutation databases

BioMutaiPGD.
DMDMi20981679.

Proteomic databases

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

Protocols and materials databases

DNASUi5226.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi5226.
DisGeNETi5226.
GeneCardsiPGD.
HGNCiHGNC:8891. PGD.
HPAiHPA031314.
HPA031315.
MIMi172200. gene.
neXtProtiNX_P52209.
OpenTargetsiENSG00000142657.
PharmGKBiPA33229.
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
BioCyciMetaCyc:HS06949-MONOMER.
ZFISH:HS06949-MONOMER.
ReactomeiR-HSA-71336. Pentose phosphate pathway (hexose monophosphate shunt).
SABIO-RKP52209.

Miscellaneous databases

ChiTaRSiPGD. human.
EvolutionaryTraceiP52209.
GenomeRNAii5226.
PROiP52209.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000142657.
CleanExiHS_PGD.
ExpressionAtlasiP52209. baseline and differential.
GenevisibleiP52209. HS.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR012284. 6PGD_dom_3.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_Gnd/GntZ.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR016040. NAD(P)-bd_dom.
IPR006183. Pgluconate_DH.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
PRINTSiPR00076. 6PGDHDRGNASE.
SMARTiSM01350. 6PGD. 1 hit.
[Graphical view]
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry namei6PGD_HUMAN
AccessioniPrimary (citable) accession number: P52209
Secondary accession number(s): A8K2Y9, B4DQJ8, Q9BWD8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 167 of the entry and version 3 of the sequence. [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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.