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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

PGD

Organism
Ovis aries (Sheep)
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.

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 (G6PD), Glucose-6-phosphate 1-dehydrogenase (g6pd)
  2. no protein annotated in this organism
  3. 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 sitei103NADP1
Binding sitei103Substrate1
Binding sitei129Substrate1
Active sitei184Proton acceptor1
Active sitei191Proton donor1
Binding sitei192Substrate1
Binding sitei261Substrate; via amide nitrogen1
Binding sitei288Substrate1
Binding sitei447Substrate; shared with dimeric partnerBy similarity1
Binding sitei453Substrate; shared with dimeric partnerBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 15NADP6
Nucleotide bindingi33 – 35NADP3
Nucleotide bindingi75 – 77NADP3
Nucleotide bindingi478 – 481NADP; shared with dimeric partnerBy similarity4

GO - Molecular functioni

  • phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB

GO - Biological processi

  • D-gluconate metabolic process Source: UniProtKB-KW
  • pentose-phosphate shunt Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

BRENDAi1.1.1.44. 2668.
SABIO-RKP00349.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:PGD
OrganismiOvis aries (Sheep)
Taxonomic identifieri9940 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeCaprinaeOvis
Proteomesi
  • UP000002356 Componenti: Unplaced

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL1169597.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000900662 – 4836-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST482

Amino acid modifications

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

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PRIDEiP00349.

Interactioni

Subunit structurei

Homodimer.2 Publications

Chemistry databases

BindingDBiP00349.

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 – 64Combined sources7
Beta strandi70 – 73Combined sources4
Helixi79 – 91Combined sources13
Beta strandi97 – 100Combined sources4
Helixi106 – 118Combined sources13
Beta strandi122 – 130Combined sources9
Helixi131 – 137Combined sources7
Beta strandi140 – 145Combined sources6
Turni147 – 149Combined sources3
Helixi150 – 160Combined sources11
Turni165 – 167Combined sources3
Beta strandi168 – 170Combined sources3
Helixi179 – 207Combined sources29
Helixi213 – 223Combined sources11
Turni224 – 228Combined sources5
Helixi231 – 241Combined sources11
Beta strandi247 – 250Combined sources4
Helixi251 – 253Combined sources3
Helixi263 – 274Combined sources12
Helixi279 – 292Combined sources14
Helixi294 – 303Combined sources10
Helixi316 – 349Combined sources34
Helixi355 – 361Combined sources7
Beta strandi364 – 366Combined sources3
Helixi372 – 382Combined sources11
Helixi389 – 391Combined sources3
Helixi393 – 416Combined sources24
Helixi421 – 434Combined sources14
Helixi440 – 451Combined sources12
Beta strandi458 – 460Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PGNX-ray2.30A2-483[»]
1PGOX-ray2.50A2-483[»]
1PGPX-ray2.50A2-483[»]
1PGQX-ray3.17A2-483[»]
2PGDX-ray2.00A2-483[»]
ProteinModelPortaliP00349.
SMRiP00349.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00349.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni129 – 131Substrate binding3
Regioni187 – 188Substrate binding2

Sequence similaritiesi

Phylogenomic databases

HOVERGENiHBG000029.
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.

P00349-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQADIALIG LAVMGQNLIL NMNDHGFVVC AFNRTVSKVD DFLANEAKGT
60 70 80 90 100
KVLGAHSLEE MVSKLKKPRR IILLVKAGQA VDNFIEKLVP LLDIGDIIID
110 120 130 140 150
GGNSEYRDTM RRCRDLKDKG ILFVGSGVSG GEDGARYGPS LMPGGNKEAW
160 170 180 190 200
PHIKAIFQGI AAKVGTGEPC CDWVGDDGAG HFVKMVHNGI EYGDMQLICE
210 220 230 240 250
AYHLMKDVLG LGHKEMAKAF EEWNKTELDS FLIEITASIL KFQDADGKHL
260 270 280 290 300
LPKIRDSAGQ KGTGKWTAIS ALEYGVPVTL IGEAVFARCL SSLKDERIQA
310 320 330 340 350
SKKLKGPQNI PFEGDKKSFL EDIRKALYAS KIISYAQGFM LLRQAATEFG
360 370 380 390 400
WTLNYGGIAL MWRGGCIIRS VFLGKIKDAF DRNPGLQNLL LDDFFKSAVE
410 420 430 440 450
NCQDSWRRAI STGVQAGIPM PCFTTALSFY DGYRHAMLPA NLIQAQRDYF
460 470 480
GAHTYELLAK PGQFIHTNWT GHGGSVSSSS YNA
Length:483
Mass (Da):52,970
Last modified:January 23, 2007 - v4
Checksum:iF4AC5DB414385F11
GO

Sequence cautioni

The sequence described in PubMed:6685125 differs from that shown. Incorrect CNBR peptide order. Many sequencing errors.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X60195 mRNA. Translation: CAA42751.1.
PIRiS15280.
S27359. DESHGC.
RefSeqiNP_001009467.1. NM_001009467.2.
UniGeneiOar.419.

Genome annotation databases

GeneIDi443541.
KEGGioas:443541.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X60195 mRNA. Translation: CAA42751.1.
PIRiS15280.
S27359. DESHGC.
RefSeqiNP_001009467.1. NM_001009467.2.
UniGeneiOar.419.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PGNX-ray2.30A2-483[»]
1PGOX-ray2.50A2-483[»]
1PGPX-ray2.50A2-483[»]
1PGQX-ray3.17A2-483[»]
2PGDX-ray2.00A2-483[»]
ProteinModelPortaliP00349.
SMRiP00349.
ModBaseiSearch...
MobiDBiSearch...

Chemistry databases

BindingDBiP00349.
ChEMBLiCHEMBL1169597.

Proteomic databases

PRIDEiP00349.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi443541.
KEGGioas:443541.

Organism-specific databases

CTDi5226.

Phylogenomic databases

HOVERGENiHBG000029.
KOiK00033.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
BRENDAi1.1.1.44. 2668.
SABIO-RKP00349.

Miscellaneous databases

EvolutionaryTraceiP00349.
PROiP00349.

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_SHEEP
AccessioniPrimary (citable) accession number: P00349
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 139 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.