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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Treponema pallidum (strain Nichols)
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.

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), Glucose-6-phosphate 1-dehydrogenase (zwf)
  2. 6-phosphogluconolactonase (pgl)
  3. 6-phosphogluconate dehydrogenase, decarboxylating (gnd), 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 sitei102NADPBy similarity1
Binding sitei102SubstrateBy similarity1
Active sitei183Proton acceptorBy similarity1
Active sitei190Proton donorBy similarity1
Binding sitei191SubstrateBy similarity1
Binding sitei260Substrate; via amide nitrogenBy similarity1
Binding sitei287SubstrateBy similarity1
Binding sitei451Substrate; shared with dimeric partnerBy similarity1
Binding sitei457Substrate; shared with dimeric partnerBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi9 – 14NADPBy similarity6
Nucleotide bindingi32 – 34NADPBy 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

UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:gnd
Ordered Locus Names:TP_0331
OrganismiTreponema pallidum (strain Nichols)
Taxonomic identifieri243276 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesSpirochaetalesSpirochaetaceaeTreponema
Proteomesi
  • UP000000811 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000900621 – 4886-phosphogluconate dehydrogenase, decarboxylatingAdd BLAST488

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi243276.TP0331.

Structurei

3D structure databases

ProteinModelPortaliO83351.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni128 – 130Substrate bindingBy similarity3
Regioni186 – 187Substrate bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.
KOiK00033.
OMAiEGEPCVT.

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.

O83351-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGADIGFIGL AVMGENLVLN IERNGFSVAV FNRTTTVVDR FLAGRAHGKR
60 70 80 90 100
ITGAHSIAEL VSLLARPRKI MLMVKAGSAV DAVIDQILPL LEKGDLVIDG
110 120 130 140 150
GNSHYQDTIR RMHALEAAGI HFIGTGVSGG EEGALRGPSL MPGGSAQAWP
160 170 180 190 200
LVSPIFCAIA AKADDGTPCC DWVGSDGAGH YVKMIHNGIE YGDMQIIAEG
210 220 230 240 250
YWFMKHALGM SYEHMHHTFT RWNTGRLHSY LIEITAAILA HQDTDGTPLL
260 270 280 290 300
EKILDAAGQK GTGRWTCVAA LEEGSPLTLI TESVMARSLS AQKQARCKAH
310 320 330 340 350
RVFGSPVKVS KAETLSAQQR EELVSALEDA LYCAKIVSYA QGFELLSHTA
360 370 380 390 400
KRRGWTLDFS RIASLWRGGC IIRSGFLSKI SAAFAQQHDL ENLVLAPFFA
410 420 430 440 450
EELKRACPGW RTIVAESVRQ ALPVPALSAA LAWFDGFTGA ALPANLLQAQ
460 470 480
RDYFGAHTYE RTDAPRGEFF HTNWTGTGGD TIAGTYSI
Length:488
Mass (Da):52,767
Last modified:November 1, 1998 - v1
Checksum:iFB69CCCA98DEE6B5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000520 Genomic DNA. Translation: AAC65319.1.
PIRiA71337.
RefSeqiWP_010881779.1. NC_021490.2.

Genome annotation databases

EnsemblBacteriaiAAC65319; AAC65319; TP_0331.
GeneIDi2611604.
KEGGitpa:TP_0331.
PATRICi20530653. VBITrePal57110_0347.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000520 Genomic DNA. Translation: AAC65319.1.
PIRiA71337.
RefSeqiWP_010881779.1. NC_021490.2.

3D structure databases

ProteinModelPortaliO83351.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243276.TP0331.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC65319; AAC65319; TP_0331.
GeneIDi2611604.
KEGGitpa:TP_0331.
PATRICi20530653. VBITrePal57110_0347.

Phylogenomic databases

eggNOGiENOG4105C7Q. Bacteria.
COG0362. LUCA.
KOiK00033.
OMAiEGEPCVT.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.

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_TREPA
AccessioniPrimary (citable) accession number: O83351
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: November 1, 1998
Last modified: November 2, 2016
This is version 110 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

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.