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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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MetaCyc Enzyme: 6-phosphogluconate dehydrogenase

Gene: gnd Accession Numbers: EG10411 (MetaCyc), b2029, ECK2024

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of 6-phosphogluconate dehydrogenase = [Gnd]2

Summary:
A null mutation in the gnd gene encoding 6-phosphogluconate dehydrogenase does not affect the growth rate significantly. However, cellular metabolism and metabolic flux is changed [Zhao04, Jiao03].

Expression of 6-phosphogluconate dehydrogenase is growth rate regulated. Regulation is both at transcriptional [Pease94] and posttranscriptional (translation initiation) [Chang95] levels.

The enzyme is a homodimer [Veronese76].

Locations: cytosol

Map Position: [2,097,886 <- 2,099,292]

Molecular Weight of Polypeptide: 51.481 kD (from nucleotide sequence)

pI: 5.3

Unification Links: ASAP:ABE-0006737 , CGSC:669 , DIP:DIP-9819N , EchoBASE:EB0406 , EcoGene:EG10411 , EcoliWiki:b2029 , ModBase:P00350 , OU-Microarray:b2029 , PortEco:gnd , Pride:P00350 , Protein Model Portal:P00350 , RefSeq:NP_416533 , RegulonDB:EG10411 , SMR:P00350 , Swiss-Model:P00350 , UniProt:P00350

Relationship Links: InterPro:IN-FAMILY:IPR006113 , InterPro:IN-FAMILY:IPR006114 , InterPro:IN-FAMILY:IPR006115 , InterPro:IN-FAMILY:IPR006184 , InterPro:IN-FAMILY:IPR008927 , InterPro:IN-FAMILY:IPR012284 , InterPro:IN-FAMILY:IPR013328 , InterPro:IN-FAMILY:IPR016040 , PDB:Structure:2ZYA , PDB:Structure:2ZYD , PDB:Structure:3FWN , Pfam:IN-FAMILY:PF00393 , Pfam:IN-FAMILY:PF03446 , Prosite:IN-FAMILY:PS00461

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006098 - pentose-phosphate shunt Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA01, Chen10]
GO:0019521 - D-gluconate metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0004616 - phosphogluconate dehydrogenase (decarboxylating) activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Chen10, Fraenkel68]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14]
GO:0042803 - protein homodimerization activity Inferred from experiment [Chen10]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01]
GO:0050661 - NADP binding Inferred by computational analysis [GOA01]
GO:0050662 - coenzyme binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism carbon utilization carbon compounds
metabolism energy metabolism, carbon pentose pwy, oxidative branch

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: 6-phosphogluconate dehydrogenase

Synonyms: phosphogluconate dehydrogenase, phosphogluconic acid dehydrogenase, 6-phosphogluconic dehydrogenase, 6-phosphogluconic carboxylase, 6PGD, P-gluconate dehydrogenase, 6-phospho-D-gluconate:NADP+ 2-oxidoreductase (decarboxylating)

EC Number: 1.1.1.44

D-gluconate 6-phosphate + NADP+ <=> D-ribulose 5-phosphate + CO2 + NADPH

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: pentose phosphate pathway , pentose phosphate pathway (oxidative branch) I

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Cofactor Binding Comment: The enzyme shows a high degree of specificity for NADP. [Veronese76]

Activators (Unknown Mechanism): Mg2+ [Comment 1]

Inhibitors (Competitive): ATP [Westwood74, Comment 2] , NADP+ [Westwood74, Comment 3]

Inhibitors (Unknown Mechanism): p-chloromercuribenzoate , 5,5'-dithio-bis-2-nitrobenzoate , fructose 1,6-bisphosphate [Comment 4] , coenzyme A , D-ribulose 5-phosphate , a heavy metal ion [Westwood74]

Kinetic Parameters:

Substrate
Km (μM)
Citations
D-gluconate 6-phosphate
93.0
[Chen10, BRENDA14]

T(opt): 55 °C [BRENDA14, Veronese76]


Sequence Features

Feature Class Location Citations Comment
Extrinsic-Sequence-Variant 2
[UniProt10]
Alternate sequence: L; UniProt: (in strain: ECOR 70);
Nucleotide-Phosphate-Binding-Region 10 -> 15
[UniProt10]
UniProt: NADP;
Extrinsic-Sequence-Variant 32
[UniProt10]
Alternate sequence: Y; UniProt: (in strain: ECOR 70);
Nucleotide-Phosphate-Binding-Region 33 -> 35
[UniProt10]
UniProt: NADP;
Extrinsic-Sequence-Variant 39
[UniProt10]
Alternate sequence: Q; UniProt: (in strain: O7:K1 / VW187);
Extrinsic-Sequence-Variant 52
[UniProt10]
Alternate sequence: D; UniProt: (in strain: ECOR 10);
Extrinsic-Sequence-Variant 55
[UniProt10]
Alternate sequence: F; UniProt: (in strain: ECOR 10);
Nucleotide-Phosphate-Binding-Region 74 -> 76
[UniProt10]
UniProt: NADP;
Extrinsic-Sequence-Variant 102
[UniProt10]
Alternate sequence: K; UniProt: (in strain: ECOR 65);
Amino-Acid-Sites-That-Bind 102
[UniProt10]
UniProt: NADP; Non-Experimental Qualifier: by similarity;
Extrinsic-Sequence-Variant 117
[UniProt10]
Alternate sequence: S; UniProt: (in strain: ECOR 70);
Extrinsic-Sequence-Variant 123 -> 125
[UniProt10]
Alternate sequence: YRY; UniProt: (in strain: O7:K1 / VW187);
Protein-Segment 128 -> 130
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Extrinsic-Sequence-Variant 170
[UniProt10]
Alternate sequence: F; UniProt: (in strain: ECOR 10);
Extrinsic-Sequence-Variant 175
[UniProt10]
Alternate sequence: S; UniProt: (in strain: ECOR 45);
Active-Site 183
[Chen10, UniProt11]
UniProt: Proton acceptor.
Protein-Segment 186 -> 187
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Active-Site 190
[Chen10, UniProt11]
UniProt: Proton donor.
Amino-Acid-Sites-That-Bind 191
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Extrinsic-Sequence-Variant 209
[UniProt10]
Alternate sequence: S; UniProt: (in strain: ECOR 68);
Extrinsic-Sequence-Variant 211
[UniProt10]
Alternate sequence: S; UniProt: (in strain: ECOR 10 and ECOR 69);
Extrinsic-Sequence-Variant 216
[UniProt10]
Alternate sequence: T; UniProt: (in strain: ECOR 67);
Amino-Acid-Sites-That-Bind 260
[UniProt10]
UniProt: Substrate; via amide nitrogen;
Amino-Acid-Sites-That-Bind 287
[UniProt10]
UniProt: Substrate;
Extrinsic-Sequence-Variant 294
[UniProt10]
Alternate sequence: E; UniProt: (in strain: ECOR 70);
Sequence-Conflict 306
[Nasoff84, UniProt10]
Alternate sequence: R; UniProt: (in Ref. 1; AAA23918);
Extrinsic-Sequence-Variant 308
[UniProt10]
Alternate sequence: G; UniProt: (in strain: ECOR 68);
Extrinsic-Sequence-Variant 313
[UniProt10]
Alternate sequence: N; UniProt: (in strain: ECOR 67);
Extrinsic-Sequence-Variant 315
[UniProt10]
Alternate sequence: G; UniProt: (in strain: ECOR 70);
Extrinsic-Sequence-Variant 325
[UniProt10]
Alternate sequence: Q; UniProt: (in strain: ECOR 69);
Extrinsic-Sequence-Variant 330
[UniProt10]
Alternate sequence: S; UniProt: (in strain: ECOR 10);
Extrinsic-Sequence-Variant 350
[UniProt10]
Alternate sequence: A; UniProt: (in strain: ECOR 10 and ECOR 69);
Extrinsic-Sequence-Variant 369
[UniProt10]
Alternate sequence: R; UniProt: (in strain: ECOR 10);
Extrinsic-Sequence-Variant 422
[UniProt10]
Alternate sequence: A; UniProt: (in strain: ECOR 10, ECOR 65, ECOR 68, ECOR 69 and ECOR 70);
Amino-Acid-Sites-That-Bind 445
[UniProt10]
UniProt: Substrate; shared with dimeric partner;
Amino-Acid-Sites-That-Bind 451
[UniProt10]
UniProt: Substrate; shared with dimeric partner;

History:
10/20/97 Gene b2029 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10411; confirmed by SwissProt match.


References

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Chang95: Chang JT, Green CB, Wolf RE (1995). "Inhibition of translation initiation on Escherichia coli gnd mRNA by formation of a long-range secondary structure involving the ribosome binding site and the internal complementary sequence." J Bacteriol 177(22);6560-7. PMID: 7592434

Chen10: Chen YY, Ko TP, Chen WH, Lo LP, Lin CH, Wang AH (2010). "Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism." J Struct Biol 169(1);25-35. PMID: 19686854

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Fraenkel68: Fraenkel DG (1968). "Selection of Escherichia coli mutants lacking glucose-6-phosphate dehydrogenase or gluconate-6-phosphate dehydrogenase." J Bacteriol 95(4);1267-71. PMID: 4869212

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jiao03: Jiao Z, Baba T, Mori H, Shimizu K (2003). "Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-13 tracer experiment and enzyme activity measurement." FEMS Microbiol Lett 220(2);295-301. PMID: 12670695

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Nasoff84: Nasoff MS, Baker HV, Wolf RE (1984). "DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase." Gene 27(3);253-64. PMID: 6329905

Pease94: Pease AJ, Wolf RE (1994). "Determination of the growth rate-regulated steps in expression of the Escherichia coli K-12 gnd gene." J Bacteriol 176(1);115-22. PMID: 8282686

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Veronese76: Veronese FM, Boccu E, Fontana A (1976). "Isolation and properties of 6-phosphogluconate dehydrogenase from Escherichia coli. Some comparisons with the thermophilic enzyme from Bacillus stearothermophilus." Biochemistry 15(18);4026-33. PMID: 786365

Westwood74: Westwood AW, Doelle HW "Glucose-6-phosphate and 6-phosphogluconate dehydrogenases and their control mechanisms in Escherichia coli K-12." Microbios 1974;9:143-165.

Zhao04: Zhao J, Baba T, Mori H, Shimizu K (2004). "Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities." Appl Microbiol Biotechnol 64(1);91-8. PMID: 14661115


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, biocyc14.