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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Shigella sonnei
Status
Reviewed-Annotation score: -Protein inferred from homologyi

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 (zwf), Glucose-6-phosphate 1-dehydrogenase (zwf), Glucose-6-phosphate 1-dehydrogenase (zwf), Glucose-6-phosphate 1-dehydrogenase (zwf)
  2. 6-phosphogluconolactonase (pgl), 6-phosphogluconolactonase (pgl), 6-phosphogluconolactonase (pgl)
  3. 6-phosphogluconate dehydrogenase, decarboxylating (CI726_04920), 6-phosphogluconate dehydrogenase, decarboxylating (CI726_27615), 6-phosphogluconate dehydrogenase, decarboxylating (CI726_25085), 6-phosphogluconate dehydrogenase, decarboxylating (CI633_28130), 6-phosphogluconate dehydrogenase, decarboxylating (CBL27_08855), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 6-phosphogluconate dehydrogenase, decarboxylating (CI641_19760)
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 sitei91NADPBy similarity1
Binding sitei91SubstrateBy similarity1
Active sitei172Proton acceptorBy similarity1
Active sitei179Proton donorBy similarity1
Binding sitei180SubstrateBy similarity1
Binding sitei249Substrate; via amide nitrogenBy similarity1
Binding sitei276SubstrateBy similarity1
Binding sitei434Substrate; shared with dimeric partnerBy similarity1
Binding sitei440Substrate; shared with dimeric partnerBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi1 – 4NADPBy similarity4
Nucleotide bindingi22 – 24NADPBy similarity3
Nucleotide bindingi63 – 65NADPBy 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 (EC:1.1.1.44)
Gene namesi
Name:gnd
OrganismiShigella sonnei
Taxonomic identifieri624 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeShigella

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_0000090051‹1 – ›4456-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST›445

Interactioni

Subunit structurei

Homodimer.By similarity

Structurei

3D structure databases

ProteinModelPortaliP41580
SMRiP41580
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni117 – 119Substrate bindingBy similarity3
Regioni175 – 176Substrate 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
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

Sequencei

Sequence statusi: Fragment.

P41580-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
AVMGRNLALN IESRGYTVSI FNRSREKTEE VIAENPGKKL VPYYTVKEFV
60 70 80 90 100
ESLETPRRIL LMVKAGAGTD AAIDSLKPYL DKGDIIIDGG NTFFQDTIRR
110 120 130 140 150
NRELSAEGFN FIGTGVSGGE EGALKGPSIM PGGQKEAYEL VAPILTKIAA
160 170 180 190 200
VAEDGEPCVT YIGADGAGHY VKMVHNGIEY GDMQLIAEAY SLLKGGLNLS
210 220 230 240 250
NEELAQTFTE WNNGELSSYL IDITKDIFTK KDEDGNYLVD VILDEAANKG
260 270 280 290 300
TGKWTSQSAL DLGEPLSLIT ESVFARYISS LKDQRVAASK VLSGPQAQSA
310 320 330 340 350
GDKAEFIEKV RRALYLGKIV SYAQGFSQLR AASEEYNWDL NYGEIAKIFR
360 370 380 390 400
AGCIIRAQFL QKITDAYAEN PQIANLLLAP YFKQIADDYQ QALRDVVAYA
410 420 430 440
VQNGIPVPTF AAAVAYYDSY RAAVLPANLI QAQRDYFGAH TYKRI
Length:445
Mass (Da):48,824
Last modified:November 1, 1995 - v1
Checksum:i07F8D753DBB0366E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Non-terminal residuei11
Non-terminal residuei4451

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U14470 Genomic DNA Translation: AAC43835.1
U14440 Genomic DNA Translation: AAC43790.1

Similar proteinsi

Entry informationi

Entry namei6PGD_SHISO
AccessioniPrimary (citable) accession number: P41580
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: May 23, 2018
This is version 88 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

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

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