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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Staphylococcus aureus (strain N315)
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.

Pathway:ipentose 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. no protein annotated in this organism
  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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei101 – 1011NADPBy similarity
Binding sitei101 – 1011SubstrateBy similarity
Active sitei182 – 1821Proton acceptorBy similarity
Active sitei189 – 1891Proton donorBy similarity
Binding sitei190 – 1901SubstrateBy similarity
Binding sitei259 – 2591Substrate; via amide nitrogenBy similarity
Binding sitei286 – 2861SubstrateBy similarity
Binding sitei444 – 4441Substrate; shared with dimeric partnerBy similarity
Binding sitei450 – 4501Substrate; shared with dimeric partnerBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi9 – 146NADPBy similarity
Nucleotide bindingi32 – 343NADPBy similarity
Nucleotide bindingi73 – 753NADPBy similarity

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

BioCyciSAUR158879:GJCB-1411-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:SA1342
OrganismiStaphylococcus aureus (strain N315)
Taxonomic identifieri158879 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcus
ProteomesiUP000000751 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4684686-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090053Add
BLAST

2D gel databases

SWISS-2DPAGEP63334.

Interactioni

Subunit structurei

Homodimer.By similarity

Structurei

3D structure databases

ProteinModelPortaliP63334.
SMRiP63334. Positions 3-467.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni127 – 1293Substrate bindingBy similarity
Regioni185 – 1862Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0362.
HOGENOMiHOG000255147.
KOiK00033.
OMAiEGEPCVT.
OrthoDBiEOG6MSS4W.

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.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P63334-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTQQIGVIGL AVMGKNLAWN IESRGYSVSV FNRSSEKTDL MVEESKGKNI
60 70 80 90 100
HPTYSLEEFV NSLEKPRKIL LMVQAGKATD ATIDSLLPLL DDGDILIDGG
110 120 130 140 150
NTNYQDTIRR NKALAQSAIN FIGMGVSGGE IGALTGPSLM PGGQEEAYNK
160 170 180 190 200
VADILDAIAA KAKDGASCVT YIGPNGAGHY VKMVHNGIEY ADMQLIAESY
210 220 230 240 250
AMMKELLGMS HEDIAQTFKD WNAGELESYL IEITGDIFMK LDENKEALVE
260 270 280 290 300
KILDTAGQKG TGKWTSINAL ELGIPLTIIT ESVFARFISS IKEERVNASK
310 320 330 340 350
ELNGPKASFD GDKKDFLEKI RKALYMSKIC SYAQGFAQMR KASEDNEWNL
360 370 380 390 400
KLGDLAMIWR EGCIIRAQFL QKIKDAYDNN PGLQNLLLDP YFKNIVTEYQ
410 420 430 440 450
DALRDVVATG VQNGVPTPGF SSSINYYDSY RAADLPANLI QAQRDYFGAH
460
TYERKDKEGV FHTQWIEE
Length:468
Mass (Da):51,803
Last modified:October 11, 2004 - v1
Checksum:i61A5C2CAF3CCD011
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000018 Genomic DNA. Translation: BAB42604.1.
PIRiG89930.
RefSeqiWP_000193707.1. NC_002745.2.

Genome annotation databases

EnsemblBacteriaiBAB42604; BAB42604; BAB42604.
GeneIDi23197318.
KEGGisau:SA1342.
PATRICi19574952. VBIStaAur116463_1445.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000018 Genomic DNA. Translation: BAB42604.1.
PIRiG89930.
RefSeqiWP_000193707.1. NC_002745.2.

3D structure databases

ProteinModelPortaliP63334.
SMRiP63334. Positions 3-467.
ModBaseiSearch...
MobiDBiSearch...

2D gel databases

SWISS-2DPAGEP63334.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB42604; BAB42604; BAB42604.
GeneIDi23197318.
KEGGisau:SA1342.
PATRICi19574952. VBIStaAur116463_1445.

Phylogenomic databases

eggNOGiCOG0362.
HOGENOMiHOG000255147.
KOiK00033.
OMAiEGEPCVT.
OrthoDBiEOG6MSS4W.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
BioCyciSAUR158879:GJCB-1411-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.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: N315.
  2. Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: N315.
  3. "Shotgun proteomic analysis of total and membrane protein extracts of S. aureus strain N315."
    Vaezzadeh A.R., Deshusses J., Lescuyer P., Hochstrasser D.F.
    Submitted (OCT-2007) to UniProtKB
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: N315.

Entry informationi

Entry namei6PGD_STAAN
AccessioniPrimary (citable) accession number: P63334
Secondary accession number(s): Q99TY2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: July 22, 2015
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

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

External Data

Dasty 3

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 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.