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P00350

- 6PGD_ECOLI

UniProt

P00350 - 6PGD_ECOLI

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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 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.1 Publication

Catalytic activityi

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

Kineticsi

  1. KM=49 µM for NADP1 Publication
  2. KM=93 µM for 6-phospho-D-gluconate1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei102 – 1021NADPBy similarity
Binding sitei102 – 1021Substrate
Active sitei183 – 1831Proton acceptor1 Publication
Active sitei190 – 1901Proton donor1 Publication
Binding sitei191 – 1911SubstrateBy similarity
Binding sitei260 – 2601Substrate; via amide nitrogen
Binding sitei287 – 2871Substrate
Binding sitei445 – 4451Substrate; shared with dimeric partner
Binding sitei451 – 4511Substrate; shared with dimeric partner

Regions

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

GO - Molecular functioni

  1. identical protein binding Source: IntAct
  2. NADP binding Source: InterPro
  3. phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB
  4. protein homodimerization activity Source: UniProtKB

GO - Biological processi

  1. D-gluconate metabolic process Source: UniProtKB-KW
  2. pentose-phosphate shunt Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

BioCyciEcoCyc:6PGLUCONDEHYDROG-MONOMER.
ECOL316407:JW2011-MONOMER.
MetaCyc:6PGLUCONDEHYDROG-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:b2029, JW2011
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10411. gnd.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4684686-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090037Add
BLAST

Proteomic databases

PRIDEiP00350.

Expressioni

Gene expression databases

GenevestigatoriP00350.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
itself4EBI-907049,EBI-907049

Protein-protein interaction databases

DIPiDIP-9819N.
IntActiP00350. 5 interactions.

Structurei

Secondary structure

1
468
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 96Combined sources
Helixi13 – 2311Combined sources
Turni24 – 263Combined sources
Beta strandi29 – 324Combined sources
Helixi36 – 4510Combined sources
Beta strandi51 – 533Combined sources
Helixi57 – 626Combined sources
Beta strandi69 – 724Combined sources
Beta strandi76 – 783Combined sources
Helixi79 – 879Combined sources
Helixi88 – 903Combined sources
Beta strandi96 – 994Combined sources
Helixi105 – 11713Combined sources
Beta strandi121 – 1299Combined sources
Helixi130 – 1367Combined sources
Beta strandi139 – 1446Combined sources
Helixi146 – 15914Combined sources
Beta strandi168 – 1703Combined sources
Helixi178 – 20831Combined sources
Helixi212 – 22413Combined sources
Turni225 – 2273Combined sources
Helixi230 – 24011Combined sources
Beta strandi246 – 2483Combined sources
Helixi249 – 2524Combined sources
Helixi265 – 2739Combined sources
Helixi278 – 29013Combined sources
Helixi293 – 3008Combined sources
Helixi314 – 34734Combined sources
Helixi353 – 3597Combined sources
Beta strandi361 – 3644Combined sources
Helixi370 – 38011Combined sources
Helixi387 – 3893Combined sources
Helixi391 – 41424Combined sources
Helixi419 – 43113Combined sources
Helixi438 – 44912Combined sources
Beta strandi455 – 4584Combined sources
Beta strandi460 – 4623Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZYAX-ray1.60A/B1-468[»]
2ZYDX-ray1.50A/B1-468[»]
3FWNX-ray1.50A/B1-468[»]
ProteinModelPortaliP00350.
SMRiP00350. Positions 2-467.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00350.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni128 – 1303Substrate binding
Regioni186 – 1872Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

InParanoidiP00350.
KOiK00033.
OMAiDKDGVFH.
OrthoDBiEOG6MSS4W.
PhylomeDBiP00350.

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.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P00350-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSKQQIGVVG MAVMGRNLAL NIESRGYTVS IFNRSREKTE EVIAENPGKK
60 70 80 90 100
LVPYYTVKEF VESLETPRRI LLMVKAGAGT DAAIDSLKPY LDKGDIIIDG
110 120 130 140 150
GNTFFQDTIR RNRELSAEGF NFIGTGVSGG EEGALKGPSI MPGGQKEAYE
160 170 180 190 200
LVAPILTKIA AVAEDGEPCV TYIGADGAGH YVKMVHNGIE YGDMQLIAEA
210 220 230 240 250
YSLLKGGLNL TNEELAQTFT EWNNGELSSY LIDITKDIFT KKDEDGNYLV
260 270 280 290 300
DVILDEAANK GTGKWTSQSA LDLGEPLSLI TESVFARYIS SLKDQRVAAS
310 320 330 340 350
KVLSGPQAQP AGDKAEFIEK VRRALYLGKI VSYAQGFSQL RAASEEYNWD
360 370 380 390 400
LNYGEIAKIF RAGCIIRAQF LQKITDAYAE NPQIANLLLA PYFKQIADDY
410 420 430 440 450
QQALRDVVAY AVQNGIPVPT FSAAVAYYDS YRAAVLPANL IQAQRDYFGA
460
HTYKRIDKEG VFHTEWLD
Length:468
Mass (Da):51,481
Last modified:November 1, 1997 - v2
Checksum:i62A32C84DC596D86
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti306 – 3061P → R in AAA23918. (PubMed:6329905)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti2 – 21S → L in strain: ECOR 70.
Natural varianti32 – 321F → Y in strain: ECOR 70.
Natural varianti39 – 391T → Q in strain: O7:K1 / VW187.
Natural varianti52 – 521V → D in strain: ECOR 10.
Natural varianti55 – 551Y → F in strain: ECOR 10.
Natural varianti102 – 1021N → K in strain: ECOR 65.
Natural varianti117 – 1171A → S in strain: ECOR 70.
Natural varianti123 – 1253IGT → YRY in strain: O7:K1 / VW187.
Natural varianti170 – 1701V → F in strain: ECOR 10.
Natural varianti175 – 1751A → S in strain: ECOR 45.
Natural varianti209 – 2091N → S in strain: ECOR 68.
Natural varianti211 – 2111T → S in strain: ECOR 10 and ECOR 69.
Natural varianti216 – 2161A → T in strain: ECOR 67.
Natural varianti294 – 2941D → E in strain: ECOR 70.
Natural varianti308 – 3081A → G in strain: ECOR 68.
Natural varianti313 – 3131D → N in strain: ECOR 67.
Natural varianti315 – 3151A → G in strain: ECOR 70.
Natural varianti325 – 3251L → Q in strain: ECOR 69.
Natural varianti330 – 3301I → S in strain: ECOR 10.
Natural varianti350 – 3501D → A in strain: ECOR 10 and ECOR 69.
Natural varianti369 – 3691Q → R in strain: ECOR 10.
Natural varianti422 – 4221S → A in strain: ECOR 10, ECOR 65, ECOR 68, ECOR 69 and ECOR 70.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02072 Genomic DNA. Translation: AAA23918.1.
M63821 Genomic DNA. Translation: AAA24488.1.
M64326 Genomic DNA. Translation: AAA24204.1.
M64327 Genomic DNA. Translation: AAA24205.1.
M64328 Genomic DNA. Translation: AAA24206.1.
M64329 Genomic DNA. Translation: AAA24207.1.
M64330 Genomic DNA. Translation: AAA24208.1.
M64331 Genomic DNA. Translation: AAA24209.1.
U00096 Genomic DNA. Translation: AAC75090.1.
AP009048 Genomic DNA. Translation: BAA15869.1.
M23181 Genomic DNA. Translation: AAA23924.1.
M18956 Genomic DNA. Translation: AAA23919.1.
M18957 Genomic DNA. Translation: AAA23920.1.
M18960 Genomic DNA. Translation: AAA23922.1.
AF125322 Genomic DNA. Translation: AAC27540.1.
PIRiD64968. DEECGC.
I62463.
I62465.
RefSeqiNP_416533.1. NC_000913.3.
YP_490272.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75090; AAC75090; b2029.
BAA15869; BAA15869; BAA15869.
GeneIDi12932360.
946554.
KEGGiecj:Y75_p1992.
eco:b2029.
PATRICi32119393. VBIEscCol129921_2106.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02072 Genomic DNA. Translation: AAA23918.1 .
M63821 Genomic DNA. Translation: AAA24488.1 .
M64326 Genomic DNA. Translation: AAA24204.1 .
M64327 Genomic DNA. Translation: AAA24205.1 .
M64328 Genomic DNA. Translation: AAA24206.1 .
M64329 Genomic DNA. Translation: AAA24207.1 .
M64330 Genomic DNA. Translation: AAA24208.1 .
M64331 Genomic DNA. Translation: AAA24209.1 .
U00096 Genomic DNA. Translation: AAC75090.1 .
AP009048 Genomic DNA. Translation: BAA15869.1 .
M23181 Genomic DNA. Translation: AAA23924.1 .
M18956 Genomic DNA. Translation: AAA23919.1 .
M18957 Genomic DNA. Translation: AAA23920.1 .
M18960 Genomic DNA. Translation: AAA23922.1 .
AF125322 Genomic DNA. Translation: AAC27540.1 .
PIRi D64968. DEECGC.
I62463.
I62465.
RefSeqi NP_416533.1. NC_000913.3.
YP_490272.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2ZYA X-ray 1.60 A/B 1-468 [» ]
2ZYD X-ray 1.50 A/B 1-468 [» ]
3FWN X-ray 1.50 A/B 1-468 [» ]
ProteinModelPortali P00350.
SMRi P00350. Positions 2-467.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9819N.
IntActi P00350. 5 interactions.

Proteomic databases

PRIDEi P00350.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75090 ; AAC75090 ; b2029 .
BAA15869 ; BAA15869 ; BAA15869 .
GeneIDi 12932360.
946554.
KEGGi ecj:Y75_p1992.
eco:b2029.
PATRICi 32119393. VBIEscCol129921_2106.

Organism-specific databases

EchoBASEi EB0406.
EcoGenei EG10411. gnd.

Phylogenomic databases

InParanoidi P00350.
KOi K00033.
OMAi DKDGVFH.
OrthoDBi EOG6MSS4W.
PhylomeDBi P00350.

Enzyme and pathway databases

UniPathwayi UPA00115 ; UER00410 .
BioCyci EcoCyc:6PGLUCONDEHYDROG-MONOMER.
ECOL316407:JW2011-MONOMER.
MetaCyc:6PGLUCONDEHYDROG-MONOMER.

Miscellaneous databases

EvolutionaryTracei P00350.
PROi P00350.

Gene expression databases

Genevestigatori P00350.

Family and domain databases

Gene3Di 1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProi IPR008927. 6-PGluconate_DH_C-like.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view ]
PIRSFi PIRSF000109. 6PGD. 1 hit.
SUPFAMi SSF48179. SSF48179. 1 hit.
TIGRFAMsi TIGR00873. gnd. 1 hit.
PROSITEi PS00461. 6PGD. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase."
    Nasoff M.S., Baker H.V. II, Wolf R.E. Jr.
    Gene 27:253-264(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus."
    Bisercic M., Feutrier J.Y., Reeves P.R.
    J. Bacteriol. 173:3894-3900(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ECOR 10.
  3. "Recombination in Escherichia coli and the definition of biological species."
    Dykhuizen D.E., Green L.
    J. Bacteriol. 173:7257-7268(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ECOR 45, ECOR 65, ECOR 67, ECOR 68, ECOR 69 and ECOR 70.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  6. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  7. "Fitness effects of a deletion mutation increasing transcription of the 6-phosphogluconate dehydrogenase gene in Escherichia coli."
    Miller R.D., Dykhuizen D.E., Hartl D.L.
    Mol. Biol. Evol. 5:691-703(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
  8. "Comparative nucleotide sequence analysis of growth-rate-regulated gnd alleles from natural isolates of Escherichia coli and from Salmonella typhimurium LT-2."
    Barcak G.J., Wolf R.E. Jr.
    J. Bacteriol. 170:372-379(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
  9. "Identification, expression, and DNA sequence of the GDP-mannose biosynthesis genes encoded by the O7 rfb gene cluster of strain VW187 (Escherichia coli O7:K1)."
    Marolda C.L., Valvano M.A.
    J. Bacteriol. 175:148-158(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
    Strain: O7:K1 / VW187.
  10. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  11. "Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism."
    Chen Y.Y., Ko T.P., Chen W.H., Lo L.P., Lin C.H., Wang A.H.
    J. Struct. Biol. 169:25-35(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEXES WITH NADP AND SUBSTRATE, SUBUNIT, CATALYTIC ACTIVITY, FUNCTION, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES.

Entry informationi

Entry namei6PGD_ECOLI
AccessioniPrimary (citable) accession number: P00350
Secondary accession number(s): P78080
, Q47571, Q59366, Q59402, Q59411, Q59412, Q59413, Q59414, Q59416, Q79DT3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 1, 1997
Last modified: November 26, 2014
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3