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P00350 (6PGD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 124. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
6-phosphogluconate dehydrogenase, decarboxylating

EC=1.1.1.44
Gene names
Name:gnd
Ordered Locus Names:b2029, JW2011
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length468 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH. Ref.11

Catalytic activity

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH. Ref.11

Pathway

Carbohydrate degradation; pentose phosphate pathway; D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 3/3.

Subunit structure

Homodimer. Ref.11

Sequence similarities

Belongs to the 6-phosphogluconate dehydrogenase family.

Biophysicochemical properties

Kinetic parameters:

KM=49 µM for NADP Ref.11

KM=93 µM for 6-phospho-D-gluconate

Binary interactions

With

Entry

#Exp.

IntAct

Notes

itself4EBI-907049,EBI-907049

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 4684686-phosphogluconate dehydrogenase, decarboxylating
PRO_0000090037

Regions

Nucleotide binding10 – 156NADP
Nucleotide binding33 – 353NADP
Nucleotide binding74 – 763NADP
Region128 – 1303Substrate binding
Region186 – 1872Substrate binding By similarity

Sites

Active site1831Proton acceptor Ref.11
Active site1901Proton donor Ref.11
Binding site1021NADP By similarity
Binding site1021Substrate
Binding site1911Substrate By similarity
Binding site2601Substrate; via amide nitrogen
Binding site2871Substrate
Binding site4451Substrate; shared with dimeric partner
Binding site4511Substrate; shared with dimeric partner

Natural variations

Natural variant21S → L in strain: ECOR 70.
Natural variant321F → Y in strain: ECOR 70.
Natural variant391T → Q in strain: O7:K1 / VW187.
Natural variant521V → D in strain: ECOR 10.
Natural variant551Y → F in strain: ECOR 10.
Natural variant1021N → K in strain: ECOR 65.
Natural variant1171A → S in strain: ECOR 70.
Natural variant123 – 1253IGT → YRY in strain: O7:K1 / VW187.
Natural variant1701V → F in strain: ECOR 10.
Natural variant1751A → S in strain: ECOR 45.
Natural variant2091N → S in strain: ECOR 68.
Natural variant2111T → S in strain: ECOR 10 and ECOR 69.
Natural variant2161A → T in strain: ECOR 67.
Natural variant2941D → E in strain: ECOR 70.
Natural variant3081A → G in strain: ECOR 68.
Natural variant3131D → N in strain: ECOR 67.
Natural variant3151A → G in strain: ECOR 70.
Natural variant3251L → Q in strain: ECOR 69.
Natural variant3301I → S in strain: ECOR 10.
Natural variant3501D → A in strain: ECOR 10 and ECOR 69.
Natural variant3691Q → R in strain: ECOR 10.
Natural variant4221S → A in strain: ECOR 10, ECOR 65, ECOR 68, ECOR 69 and ECOR 70.

Experimental info

Sequence conflict3061P → R in AAA23918. Ref.1

Secondary structure

..................................................................... 468
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P00350 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 62A32C84DC596D86

FASTA46851,481
        10         20         30         40         50         60 
MSKQQIGVVG MAVMGRNLAL NIESRGYTVS IFNRSREKTE EVIAENPGKK LVPYYTVKEF 

        70         80         90        100        110        120 
VESLETPRRI LLMVKAGAGT DAAIDSLKPY LDKGDIIIDG GNTFFQDTIR RNRELSAEGF 

       130        140        150        160        170        180 
NFIGTGVSGG EEGALKGPSI MPGGQKEAYE LVAPILTKIA AVAEDGEPCV TYIGADGAGH 

       190        200        210        220        230        240 
YVKMVHNGIE YGDMQLIAEA YSLLKGGLNL TNEELAQTFT EWNNGELSSY LIDITKDIFT 

       250        260        270        280        290        300 
KKDEDGNYLV DVILDEAANK GTGKWTSQSA LDLGEPLSLI TESVFARYIS SLKDQRVAAS 

       310        320        330        340        350        360 
KVLSGPQAQP AGDKAEFIEK VRRALYLGKI VSYAQGFSQL RAASEEYNWD LNYGEIAKIF 

       370        380        390        400        410        420 
RAGCIIRAQF LQKITDAYAE NPQIANLLLA PYFKQIADDY QQALRDVVAY AVQNGIPVPT 

       430        440        450        460 
FSAAVAYYDS YRAAVLPANL IQAQRDYFGA HTYKRIDKEG VFHTEWLD 

« Hide

References

« Hide 'large scale' references
[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]"A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map."
Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S. expand/collapse author list , Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:379-392(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRDEECGC. D64968.
I62463.
I62465.
RefSeqNP_416533.1. NC_000913.3.
YP_490272.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZYAX-ray1.60A/B1-468[»]
2ZYDX-ray1.50A/B1-468[»]
3FWNX-ray1.50A/B1-468[»]
ProteinModelPortalP00350.
SMRP00350. Positions 2-467.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9819N.
IntActP00350. 5 interactions.

Proteomic databases

PRIDEP00350.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75090; AAC75090; b2029.
BAA15869; BAA15869; BAA15869.
GeneID12932360.
946554.
KEGGecj:Y75_p1992.
eco:b2029.
PATRIC32119393. VBIEscCol129921_2106.

Organism-specific databases

EchoBASEEB0406.
EcoGeneEG10411. gnd.

Phylogenomic databases

KOK00033.
OMAKQQIGVI.
OrthoDBEOG6MSS4W.
ProtClustDBPRK09287.

Enzyme and pathway databases

BioCycEcoCyc:6PGLUCONDEHYDROG-MONOMER.
ECOL316407:JW2011-MONOMER.
MetaCyc:6PGLUCONDEHYDROG-MONOMER.
UniPathwayUPA00115; UER00410.

Gene expression databases

GenevestigatorP00350.

Family and domain databases

Gene3D1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProIPR008927. 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]
PfamPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFPIRSF000109. 6PGD. 1 hit.
SUPFAMSSF48179. SSF48179. 1 hit.
TIGRFAMsTIGR00873. gnd. 1 hit.
PROSITEPS00461. 6PGD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP00350.
PROP00350.

Entry information

Entry name6PGD_ECOLI
AccessionPrimary (citable) accession number: P00350
Secondary accession number(s): P78080 expand/collapse secondary AC list , Q47571, Q59366, Q59402, Q59411, Q59412, Q59413, Q59414, Q59416, Q79DT3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 124 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene