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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
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 (zwf)
  2. no protein annotated in this organism
  3. 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 sitei103NADPBy similarity1
Binding sitei103SubstrateBy similarity1
Active sitei183Proton acceptorBy similarity1
Active sitei190Proton donorBy similarity1
Binding sitei191SubstrateBy similarity1
Binding sitei263Substrate; via amide nitrogenBy similarity1
Binding sitei290SubstrateBy similarity1
Binding sitei449Substrate; shared with dimeric partnerBy similarity1
Binding sitei455Substrate; shared with dimeric partnerBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 15NADPBy similarity6
Nucleotide bindingi33 – 35NADPBy similarity3
Nucleotide bindingi75 – 77NADPBy 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

BioCyciSYNEL:SYNPCC7942_0039-MONOMER.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:gnd
Ordered Locus Names:Synpcc7942_0039
OrganismiSynechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
Taxonomic identifieri1140 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaSynechococcalesSynechococcaceaeSynechococcus
Proteomesi
  • UP000002717 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000900601 – 4716-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST471

Proteomic databases

PRIDEiP21577.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi1140.Synpcc7942_0039.

Structurei

3D structure databases

ProteinModelPortaliP21577.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni129 – 131Substrate bindingBy similarity3
Regioni186 – 187Substrate bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.
HOGENOMiHOG000255147.
KOiK00033.
OrthoDBiPOG091H01QF.

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.

P21577-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALQQFGLIG LAVMGENLAL NIERNGFSLT VYNRTAEKTE AFMADRAQGK
60 70 80 90 100
NIVPAYSLED FVASLERPRR ILVMVKAGGP VDAVVEQLKP LLDPGDLIID
110 120 130 140 150
GGNSLFTDTE RRVKDLEALG LGFMGMGVSG GEEGALNGPS LMPGGTQAAY
160 170 180 190 200
EAVEPIVRSI AAQVDDGPCV TYIGPGGSGH YVKMVHNGIE YGDMQLIAEA
210 220 230 240 250
YDLLKSVAGL NASELHDVFA AWNKTPELDS FLIEITADIF TKVDDLGTGQ
260 270 280 290 300
PLVELILDAA GQKGTGRWTV ETALEIGVAI PTIIAAVNAR ILSSIKAERQ
310 320 330 340 350
AASEILSGPI TEPFSGDRQA FIDSVRDALY CSKICSYAQG MALLAKASQV
360 370 380 390 400
YNYGLNLGEL ARIWKGGCII RAGFLNKIKQ AYDADPTLAN LLLAPEFRQT
410 420 430 440 450
ILDRQLAWRR VIAIAAERGI PVPAFSASLD YFDSYRRDRL PQNLTQAQRD
460 470
YFGAHTYERT DRSGSFHAQW F
Length:471
Mass (Da):51,073
Last modified:April 18, 2006 - v4
Checksum:i0C75D58209E124E7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti154 – 159EPIVRS → SRSVPT in AAA27330 (PubMed:2113917).Curated6
Sequence conflicti159S → T in CAA41555 (Ref. 2) Curated1
Sequence conflicti407A → R in CAA41555 (Ref. 2) Curated1
Sequence conflicti415 – 439AAERG…YRRDR → RQNEEFRFRFQCFPGLLRQL PARS in CAA41555 (Ref. 2) CuratedAdd BLAST25
Sequence conflicti437 – 441RDRLP → ASPA in AAA27330 (PubMed:2113917).Curated5
Sequence conflicti450 – 453DYFG → TTC in AAA27330 (PubMed:2113917).Curated4
Sequence conflicti458 – 465ERTDRSGS → KAPIALL in AAA27330 (PubMed:2113917).Curated8
Sequence conflicti469 – 470QW → M in AAA27330 (PubMed:2113917).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M55002 Genomic DNA. Translation: AAA27330.1.
X58719 Genomic DNA. Translation: CAA41555.1.
CP000100 Genomic DNA. Translation: ABB56071.1.
PIRiS14628.
RefSeqiWP_011377413.1. NC_007604.1.

Genome annotation databases

EnsemblBacteriaiABB56071; ABB56071; Synpcc7942_0039.
KEGGisyf:Synpcc7942_0039.
PATRICi23785105. VBISynElo51371_0103.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M55002 Genomic DNA. Translation: AAA27330.1.
X58719 Genomic DNA. Translation: CAA41555.1.
CP000100 Genomic DNA. Translation: ABB56071.1.
PIRiS14628.
RefSeqiWP_011377413.1. NC_007604.1.

3D structure databases

ProteinModelPortaliP21577.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi1140.Synpcc7942_0039.

Proteomic databases

PRIDEiP21577.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABB56071; ABB56071; Synpcc7942_0039.
KEGGisyf:Synpcc7942_0039.
PATRICi23785105. VBISynElo51371_0103.

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.
HOGENOMiHOG000255147.
KOiK00033.
OrthoDBiPOG091H01QF.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
BioCyciSYNEL:SYNPCC7942_0039-MONOMER.

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_SYNE7
AccessioniPrimary (citable) accession number: P21577
Secondary accession number(s): Q31S98
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: April 18, 2006
Last modified: November 2, 2016
This is version 113 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic 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.