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Protein

6-phosphogluconate dehydrogenase, decarboxylating 1

Gene

pgdC

Organism
Spinacia oleracea (Spinach)
Status
Reviewed-Annotation score: Annotation score: 3 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 (G6PD), Glucose-6-phosphate 1-dehydrogenase, chloroplastic (G6PD), Glucose-6-phosphate 1-dehydrogenase (SOVF_162250), Glucose-6-phosphate 1-dehydrogenase (SOVF_004890), Glucose-6-phosphate 1-dehydrogenase (SOVF_183760)
  2. no protein annotated in this organism
  3. 6-phosphogluconate dehydrogenase, decarboxylating 2, chloroplastic (pgdP), 6-phosphogluconate dehydrogenase, decarboxylating (SOVF_090000), 6-phosphogluconate dehydrogenase, decarboxylating (SOVF_128490), 6-phosphogluconate dehydrogenase, decarboxylating 1 (pgdC)
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 sitei106NADPBy similarity1
Binding sitei106SubstrateBy similarity1
Active sitei186Proton acceptorBy similarity1
Active sitei193Proton donorBy similarity1
Binding sitei194SubstrateBy similarity1
Binding sitei264Substrate; via amide nitrogenBy similarity1
Binding sitei291SubstrateBy similarity1
Binding sitei454Substrate; shared with dimeric partnerBy similarity1
Binding sitei460Substrate; shared with dimeric partnerBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi11 – 16NADPBy similarity6
Nucleotide bindingi34 – 36NADPBy similarity3
Nucleotide bindingi78 – 80NADPBy similarity3

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
Biological processGluconate utilization, Pentose shunt
LigandNADP

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating 1 (EC:1.1.1.44)
Gene namesi
Name:pgdC
OrganismiSpinacia oleracea (Spinach)
Taxonomic identifieri3562 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesChenopodiaceaeChenopodioideaeAnserineaeSpinacia

Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004211031 – 4836-phosphogluconate dehydrogenase, decarboxylating 1Add BLAST483

Proteomic databases

PRIDEiQ94KU1.

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

3D structure databases

ProteinModelPortaliQ94KU1.
SMRiQ94KU1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni132 – 134Substrate bindingBy similarity3
Regioni189 – 190Substrate bindingBy similarity2

Sequence similaritiesi

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.
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.

Sequencei

Sequence statusi: Complete.

Q94KU1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPPTRIGLA GLAVMGQNLA LNIAEKGFPI SVYNRTTSKV DETVERAKQE
60 70 80 90 100
GNLPLYGFHD PESFVNSIQK PRVIIMLVKA GAPVDATIKT LSAYLEKGDC
110 120 130 140 150
IIDGGNEWYE NTERREKAME EKGLLYLGMG VSGGEEGARN GPSMMPGGSF
160 170 180 190 200
DAYKNIEDIL TKVAAQVDSG PCVTYIGKGG SGNFVKMIHN GIEYGDMQLI
210 220 230 240 250
AEAYDVLKSV GKLSNEELKE VFAEWNRGEL LSFLIEITAD IFGIKDDKGE
260 270 280 290 300
GYLVDKVLDK TGMKGTGKWT VQQAAELSVA APTIASSLDS RFLSGLKDER
310 320 330 340 350
VEAAKVFKAG GVEDTLSDQV VDKKKLIDDV RQALYAAKIC SYAQGMNLIR
360 370 380 390 400
AKSVEKEWDL KLGELARIWK GGCIIRAMFL DRIKKAYDRN PNLSNLLIDP
410 420 430 440 450
EFSKEMIERQ SAWRRVVCLA IGAGISTPGM SSSLAYFDSY RRERLPANLV
460 470 480
QAQRDYFGAH TYERIDIPGA FHTEWFKLAK SKI
Length:483
Mass (Da):53,245
Last modified:December 1, 2001 - v1
Checksum:iA2E5CBB1C442D45F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF307144 mRNA. Translation: AAK51690.1.

Similar proteinsi

Entry informationi

Entry namei6PGD1_SPIOL
AccessioniPrimary (citable) accession number: Q94KU1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 6, 2013
Last sequence update: December 1, 2001
Last modified: November 22, 2017
This is version 81 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families