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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Citrobacter koseri (Citrobacter diversus)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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)
  2. 6-phosphogluconolactonase (pgl)
  3. 6-phosphogluconate dehydrogenase, decarboxylating (BN1086_00776), 6-phosphogluconate dehydrogenase, decarboxylating (gnd)
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

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

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
OrganismiCitrobacter koseri (Citrobacter diversus)
Taxonomic identifieri545 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeCitrobacter

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_0000090035‹1 – ›4456-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST›445

Proteomic databases

PRIDEiP41582.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi290338.CKO_00756.

Structurei

3D structure databases

ProteinModelPortaliP41582.
SMRiP41582.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni117 – 119Substrate bindingBy similarity3
Regioni175 – 176Substrate bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.

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: Fragment.

P41582-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
AVMGRNLALN IESRGYTVSV 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
NEELAETFTE WNKGELNSYL IDITKDIFTK KDEEGKYLVD VILDEAANKG
260 270 280 290 300
TGKWTSQSSL DLGEPLSLIT ESVFARYISS LKEQRVAASK VLSGPKAQLA
310 320 330 340 350
GDKAEFIEKV RRALYLGKIV SYAQGFSQLR AASDEYNWDL NYGEIAKIFR
360 370 380 390 400
AGCIIRAQFL QKITDAYAEN AGIANLLLAP YFKKIADDYQ QALRDVVAYA
410 420 430 440
VQNGIPVPTF SAAVAYYDSY RAAVLPANLI QAQRDYFGAH TYKRT
Length:445
Mass (Da):48,829
Last modified:November 1, 1995 - v1
Checksum:i9DB96925EC40EDC4
GO

Experimental Info

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

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti31V → G in strain: CT45. 1
Natural varianti206E → D in strain: CT42. 1
Natural varianti300A → E in strain: CT27. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U14424 Genomic DNA. Translation: AAC43774.1.
U14425 Genomic DNA. Translation: AAC43775.1.
U14427 Genomic DNA. Translation: AAC43776.1.
U14428 Genomic DNA. Translation: AAC43777.1.
U14429 Genomic DNA. Translation: AAC43778.1.
U14432 Genomic DNA. Translation: AAC43779.1.
PIRiI40681.
I40682.
I40684.
I40685.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U14424 Genomic DNA. Translation: AAC43774.1.
U14425 Genomic DNA. Translation: AAC43775.1.
U14427 Genomic DNA. Translation: AAC43776.1.
U14428 Genomic DNA. Translation: AAC43777.1.
U14429 Genomic DNA. Translation: AAC43778.1.
U14432 Genomic DNA. Translation: AAC43779.1.
PIRiI40681.
I40682.
I40684.
I40685.

3D structure databases

ProteinModelPortaliP41582.
SMRiP41582.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi290338.CKO_00756.

Proteomic databases

PRIDEiP41582.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.

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_CITKO
AccessioniPrimary (citable) accession number: P41582
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: November 2, 2016
This is version 89 of the entry and version 1 of the sequence. [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

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.