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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
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.

Pathway: 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 (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 sitei102 – 1021NADPBy similarity
Binding sitei102 – 1021SubstrateBy 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 sitei445 – 4451Substrate; shared with dimeric partnerBy similarity
Binding sitei451 – 4511Substrate; shared with dimeric partnerBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 156NADPBy similarity
Nucleotide bindingi33 – 353NADPBy similarity
Nucleotide bindingi74 – 763NADPBy 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

BioCyciBAPH224915:GJ9D-101-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:bbp_101
OrganismiBuchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
Taxonomic identifieri224915 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeBuchnera
ProteomesiUP000000601 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4684686-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090030Add
BLAST

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi224915.bbp101.

Structurei

3D structure databases

ProteinModelPortaliQ89AX5.
SMRiQ89AX5. Positions 1-468.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni128 – 1303Substrate bindingBy similarity
Regioni185 – 1862Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0362.
KOiK00033.
OMAiSDEYNWD.
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.

Q89AX5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKQQIGVIG MAVMGRNLAL NMERNQYTVS IFNRSLDITE KIILNNPNKN
60 70 80 90 100
LFPFFSIKDF VLSLIVPRCI VLMIKSGVAT DDTIKSLIPY LSKGDIIIDG
110 120 130 140 150
GNTFYKDTIQ RGYELLKIGV NLIGAGFSGG EKGALYGPSI MPGGRQEAYN
160 170 180 190 200
YVSPILKKIA SNSEGIPCVT YIGPDGSGHY VKMVHNGIEY GDMQLIAESY
210 220 230 240 250
FILKTLLRLD NQSISKIFDI WNQGELNSYL IDITKDILIK KDDQNNYLID
260 270 280 290 300
CILDEGSSKG TGTWTTKSAL DLNEPLTLIT ESVFFRYLSS LKSQRLLASK
310 320 330 340 350
ILCGPKDFFI VLNRDDFIEK IRQALYLGKI ISYAQGFSQL NSASQKYNWN
360 370 380 390 400
LKLGEISRIF QSGCIIRAKL LKNITQEYSS NNNFVNLLLT PYFREIANTY
410 420 430 440 450
HSSLREIVSI SVKYGIPIPA LSSAISYFDS YRSAFLPSNL IQAQRDFFGA
460
HTYKRIDKSG IFHTNWYS
Length:468
Mass (Da):52,646
Last modified:May 30, 2003 - v1
Checksum:iC28B8C09CCB64E11
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016826 Genomic DNA. Translation: AAO26836.1.
RefSeqiNP_777731.1. NC_004545.1.
WP_011091237.1. NC_004545.1.

Genome annotation databases

EnsemblBacteriaiAAO26836; AAO26836; bbp_101.
KEGGibab:bbp101.
PATRICi21244981. VBIBucAph80364_0098.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016826 Genomic DNA. Translation: AAO26836.1.
RefSeqiNP_777731.1. NC_004545.1.
WP_011091237.1. NC_004545.1.

3D structure databases

ProteinModelPortaliQ89AX5.
SMRiQ89AX5. Positions 1-468.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224915.bbp101.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO26836; AAO26836; bbp_101.
KEGGibab:bbp101.
PATRICi21244981. VBIBucAph80364_0098.

Phylogenomic databases

eggNOGiCOG0362.
KOiK00033.
OMAiSDEYNWD.
OrthoDBiEOG6MSS4W.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
BioCyciBAPH224915:GJ9D-101-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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bp.

Entry informationi

Entry namei6PGD_BUCBP
AccessioniPrimary (citable) accession number: Q89AX5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2003
Last sequence update: May 30, 2003
Last modified: April 29, 2015
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

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

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.