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Protein

6-phosphogluconate dehydrogenase, NADP(+)-dependent, decarboxylating

Gene

gndA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 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. Is the predominant 6-P-gluconate dehydrogenase isoenzyme in B.subtilis during growth on glucose and gluconate.1 Publication

Catalytic activityi

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH.1 Publication

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, NADP(+)-dependent, decarboxylating (gndA)
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 sitei102NADPBy similarity1
Binding sitei102SubstrateBy similarity1
Active sitei182Proton acceptorBy similarity1
Active sitei189Proton donorBy similarity1
Binding sitei190SubstrateBy similarity1
Binding sitei260Substrate; via amide nitrogenBy similarity1
Binding sitei287SubstrateBy similarity1
Binding sitei446Substrate; shared with dimeric partnerBy similarity1
Binding sitei452Substrate; shared with dimeric partnerBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 15NADPBy similarity6
Nucleotide bindingi33 – 35NADPBy similarity3
Nucleotide bindingi74 – 76NADPBy 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

BioCyciBSUB:BSU23860-MONOMER.
MetaCyc:MONOMER-6842.
BRENDAi1.1.1.44. 658.
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, NADP(+)-dependent, decarboxylating (EC:1.1.1.44)
Alternative name(s):
GNTZII
Gene namesi
Name:gndA
Synonyms:yqjI
Ordered Locus Names:BSU23860
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene exhibit a reduced growth on glucose as the sole carbon source, and they do not use the pentose phosphate (PP) pathway at all.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000900272 – 4696-phosphogluconate dehydrogenase, NADP(+)-dependent, decarboxylatingAdd BLAST468

Proteomic databases

PaxDbiP80859.
PRIDEiP80859.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

IntActiP80859. 1 interactor.
MINTiMINT-8364930.
STRINGi224308.Bsubs1_010100013091.

Structurei

3D structure databases

ProteinModelPortaliP80859.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni128 – 130Substrate bindingBy similarity3
Regioni185 – 186Substrate bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.
HOGENOMiHOG000255147.
InParanoidiP80859.
KOiK00033.
OMAiEGEPCVT.
PhylomeDBiP80859.

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.

P80859-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKQQIGVIG LAVMGKNLAL NIESRGFSVS VYNRSSSKTE EFLQEAKGKN
60 70 80 90 100
VVGTYSIEEF VQSLETPRKI LLMVKAGTAT DATIQSLLPH LEKDDILIDG
110 120 130 140 150
GNTYYKDTQR RNKELAESGI HFIGTGVSGG EEGALKGPSI MPGGQKEAHE
160 170 180 190 200
LVKPILEAIS AKVDGEPCTT YIGPDGAGHY VKMVHNGIEY GDMQLISESY
210 220 230 240 250
FILKQVLGLS ADELHEVFAE WNKGELDSYL IEITADIFTK KDEETGKPLV
260 270 280 290 300
DVILDKAGQK GTGKWTSQSA LDLGVPLPII TESVFARFIS AMKEERVKAS
310 320 330 340 350
GLLSGPEVKP VTENKEELIE AVRKALFMSK ICSYAQGFAQ MKAASEEYNW
360 370 380 390 400
DLKYGEIAMI FRGGCIIRAA FLQKIKEAYD REPELDNLLL DSYFKNIVES
410 420 430 440 450
YQGALRQVIS LAVAQGVPVP SFSSALAYYD SYRTAVLPAN LIQAQRDYFG
460
AHTYERTDKE GIFHTEWMK
Length:469
Mass (Da):51,775
Last modified:January 23, 2007 - v4
Checksum:iD0A94E0B4F2250EF
GO

Sequence cautioni

The sequence BAA12615 differs from that shown. Reason: Frameshift at position 42.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti11L → W AA sequence (PubMed:9298659).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D84432 Genomic DNA. Translation: BAA12615.1. Frameshift.
AL009126 Genomic DNA. Translation: CAB14318.2.
PIRiA69964.
RefSeqiNP_390267.2. NC_000964.3.
WP_003230365.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB14318; CAB14318; BSU23860.
GeneIDi938695.
KEGGibsu:BSU23860.
PATRICi18976597. VBIBacSub10457_2489.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D84432 Genomic DNA. Translation: BAA12615.1. Frameshift.
AL009126 Genomic DNA. Translation: CAB14318.2.
PIRiA69964.
RefSeqiNP_390267.2. NC_000964.3.
WP_003230365.1. NZ_JNCM01000036.1.

3D structure databases

ProteinModelPortaliP80859.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP80859. 1 interactor.
MINTiMINT-8364930.
STRINGi224308.Bsubs1_010100013091.

Proteomic databases

PaxDbiP80859.
PRIDEiP80859.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14318; CAB14318; BSU23860.
GeneIDi938695.
KEGGibsu:BSU23860.
PATRICi18976597. VBIBacSub10457_2489.

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.
HOGENOMiHOG000255147.
InParanoidiP80859.
KOiK00033.
OMAiEGEPCVT.
PhylomeDBiP80859.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
BioCyciBSUB:BSU23860-MONOMER.
MetaCyc:MONOMER-6842.
BRENDAi1.1.1.44. 658.

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_BACSU
AccessioniPrimary (citable) accession number: P80859
Secondary accession number(s): P54546
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 128 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, Direct protein sequencing, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.