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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

Pgd

Organism
Rattus norvegicus (Rat)
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.By similarity

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).By similarity
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. Glucose-6-phosphate 1-dehydrogenase (G6pdx)
  2. 6-phosphogluconolactonase (Pgls)
  3. 6-phosphogluconate dehydrogenase, decarboxylating (Kif1b), 6-phosphogluconate dehydrogenase, decarboxylating (Pgd), 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 sitei103NADPBy similarity1
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 – 15NADPBy similarity6
Nucleotide bindingi33 – 35NADPBy similarity3
Nucleotide bindingi75 – 77NADPBy similarity3
Nucleotide bindingi478 – 481NADP; shared with dimeric partnerBy similarity4

GO - Molecular functioni

  • carbohydrate binding Source: RGD
  • carboxylic acid binding Source: RGD
  • NADP binding Source: RGD
  • phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB

GO - Biological processi

  • carbohydrate metabolic process Source: RGD
  • D-gluconate metabolic process Source: RGD
  • NADP metabolic process Source: RGD
  • pentose-phosphate shunt Source: UniProtKB
  • pentose-phosphate shunt, oxidative branch Source: RGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

SABIO-RKP85968.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylatingBy similarity (EC:1.1.1.44)
Gene namesi
Name:PgdBy similarity
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi1583832. Pgd.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • intracellular membrane-bounded organelle Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00003491152 – 4836-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST482

Amino acid modifications

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

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PRIDEiP85968.

2D gel databases

World-2DPAGE0004:P85968.

PTM databases

iPTMnetiP85968.
PhosphoSitePlusiP85968.

Expressioni

Gene expression databases

BgeeiENSRNOG00000030317.

Interactioni

Subunit structurei

Homodimer.By similarity

Structurei

3D structure databases

ProteinModelPortaliP85968.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the 6-phosphogluconate dehydrogenase family.Sequence analysis

Phylogenomic databases

HOGENOMiHOG000255147.
HOVERGENiHBG000029.
InParanoidiP85968.
KOiK00033.

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]

Sequencei

Sequence statusi: Complete.

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

P85968-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQADIALIG LAVMGQNLIL NMNDHGFVVC AFNRTVSKVD DFLAKEAKGT
60 70 80 90 100
KVIGAKSLKD MVSKLKKPRR VILLVKAGQA VDDFIEKLVP LLDTGDIIID
110 120 130 140 150
GGNSEYRDTT RRCQDLKAKG ILFVGSGVSG GEEGARYGPS LMPGGNKEAW
160 170 180 190 200
PHIKTIFQAI AAKVGTGEPC CDWVGDEGAG HFVKMVHNGI EYGDMQLICE
210 220 230 240 250
AYHLMKDVLG MRHEEMAQAF EDWNKTELDS FLIEITANIL KFQDTDGKEL
260 270 280 290 300
LPKIRDSAGQ KGTGKWTAIS ALEYGMPVTL IGEAVFARCL SSLKEERVQA
310 320 330 340 350
SRKLKGPKMV QLEGSKQAFL EDVRKALYAS KIISYAQGFM LLRQAATEFG
360 370 380 390 400
WTLNYGGIAL MWRGGCIIRS VFLGKIKDAF ERNPELQNLL LDDFFKSAVD
410 420 430 440 450
DCQDSWRRVI STGVQAGIPM PCFTTALSFY DGYRHEMLPA NLIQAQRDYF
460 470 480
GAHTYELLSK PGEFIHTNWT GHGGSVSSSS YNA
Length:483
Mass (Da):53,236
Last modified:September 2, 2008 - v1
Checksum:i7B3F308C3E9B17D4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AABR03040409 Genomic DNA. No translation available.
RefSeqiNP_001292364.1. NM_001305435.1.
UniGeneiRn.231871.

Genome annotation databases

GeneIDi100360180.
KEGGirno:100360180.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AABR03040409 Genomic DNA. No translation available.
RefSeqiNP_001292364.1. NM_001305435.1.
UniGeneiRn.231871.

3D structure databases

ProteinModelPortaliP85968.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

iPTMnetiP85968.
PhosphoSitePlusiP85968.

2D gel databases

World-2DPAGE0004:P85968.

Proteomic databases

PRIDEiP85968.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100360180.
KEGGirno:100360180.

Organism-specific databases

CTDi5226.
RGDi1583832. Pgd.

Phylogenomic databases

HOGENOMiHOG000255147.
HOVERGENiHBG000029.
InParanoidiP85968.
KOiK00033.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
SABIO-RKP85968.

Miscellaneous databases

PROiP85968.

Gene expression databases

BgeeiENSRNOG00000030317.

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_RAT
AccessioniPrimary (citable) accession number: P85968
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: September 2, 2008
Last modified: November 2, 2016
This is version 67 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.