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Protein

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

Gene

gndA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionOxidoreductase
Biological processGluconate utilization, Pentose shunt
LigandNADP

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
MINTiP80859
STRINGi224308.Bsubs1_010100013091

Structurei

3D structure databases

ProteinModelPortaliP80859
SMRiP80859
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
OMAiNSHYPDS
PhylomeDBiP80859

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: 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
PATRICifig|224308.179.peg.2599

Similar proteinsi

Entry informationi

Entry namei6PGD_BACSU
AccessioniPrimary (citable) accession number: P80859
Secondary accession number(s): P54546
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: February 28, 2018
This is version 134 of the entry and version 4 of the sequence. See 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

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