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Escherichia coli K-12 substr. MG1655 Enzyme: 6-phosphogluconate dehydrogenase



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

Regulation Summary Diagram: ?

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].

Gene Citations: [Nasoff84]

Locations: cytosol

Map Position: [2,097,886 <- 2,099,292] (45.22 centisomes)
Length: 1407 bp / 468 aa

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

In Paralogous Gene Group: 369 (5 members) , 560 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006098 - pentose-phosphate shunt Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA01a, Chen10a]
GO:0019521 - D-gluconate metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004616 - phosphogluconate dehydrogenase (decarboxylating) activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Chen10a, Fraenkel68]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14]
GO:0042803 - protein homodimerization activity Inferred from experiment [Chen10a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01a]
GO:0050661 - NADP binding Inferred by computational analysis [GOA01a]
GO:0050662 - coenzyme binding Inferred by computational analysis [GOA01a]
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

Essentiality data for gnd knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

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

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

Activators (Unknown Mechanism): Mg2+ [Comment 5]

Inhibitors (Competitive): ATP [Westwood74, Comment 6] , NADP+ [Westwood74, Comment 7]

Inhibitors (Unknown Mechanism): p-chloromercuribenzoate , 5,5'-dithio-bis-2-nitrobenzoate , fructose 1,6-bisphosphate [Comment 8] , coenzyme A , D-ribulose 5-phosphate , a heavy metal ion [Westwood74]

Kinetic Parameters:

Substrate
Km (μM)
Citations
D-gluconate 6-phosphate
93.0
[Chen10a, BRENDA14]

T(opt): 55 °C [BRENDA14, Veronese76]


Sequence Features

Feature Class Location Citations Comment
Extrinsic-Sequence-Variant 2
[UniProt10]
Alternate sequence: S → L; UniProt: (in strain: ECOR 70);
Nucleotide-Phosphate-Binding-Region 10 -> 15
[UniProt10]
UniProt: NADP;
Extrinsic-Sequence-Variant 32
[UniProt10]
Alternate sequence: F → Y; UniProt: (in strain: ECOR 70);
Nucleotide-Phosphate-Binding-Region 33 -> 35
[UniProt10]
UniProt: NADP;
Extrinsic-Sequence-Variant 39
[UniProt10]
Alternate sequence: T → Q; UniProt: (in strain: O7:K1 / VW187);
Extrinsic-Sequence-Variant 52
[UniProt10]
Alternate sequence: V → D; UniProt: (in strain: ECOR 10);
Extrinsic-Sequence-Variant 55
[UniProt10]
Alternate sequence: Y → F; UniProt: (in strain: ECOR 10);
Nucleotide-Phosphate-Binding-Region 74 -> 76
[UniProt10]
UniProt: NADP;
Extrinsic-Sequence-Variant 102
[UniProt10]
Alternate sequence: N → 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: A → S; UniProt: (in strain: ECOR 70);
Extrinsic-Sequence-Variant 123 -> 125
[UniProt10]
Alternate sequence: IGT → 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: V → F; UniProt: (in strain: ECOR 10);
Extrinsic-Sequence-Variant 175
[UniProt10]
Alternate sequence: A → S; UniProt: (in strain: ECOR 45);
Active-Site 183
[Chen10a, 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
[Chen10a, 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: N → S; UniProt: (in strain: ECOR 68);
Extrinsic-Sequence-Variant 211
[UniProt10]
Alternate sequence: T → S; UniProt: (in strain: ECOR 10 and ECOR 69);
Extrinsic-Sequence-Variant 216
[UniProt10]
Alternate sequence: A → 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: D → E; UniProt: (in strain: ECOR 70);
Sequence-Conflict 306
[Nasoff84, UniProt10]
Alternate sequence: P → R; UniProt: (in Ref. 1; AAA23918);
Extrinsic-Sequence-Variant 308
[UniProt10]
Alternate sequence: A → G; UniProt: (in strain: ECOR 68);
Extrinsic-Sequence-Variant 313
[UniProt10]
Alternate sequence: D → N; UniProt: (in strain: ECOR 67);
Extrinsic-Sequence-Variant 315
[UniProt10]
Alternate sequence: A → G; UniProt: (in strain: ECOR 70);
Extrinsic-Sequence-Variant 325
[UniProt10]
Alternate sequence: L → Q; UniProt: (in strain: ECOR 69);
Extrinsic-Sequence-Variant 330
[UniProt10]
Alternate sequence: I → S; UniProt: (in strain: ECOR 10);
Extrinsic-Sequence-Variant 350
[UniProt10]
Alternate sequence: D → A; UniProt: (in strain: ECOR 10 and ECOR 69);
Extrinsic-Sequence-Variant 369
[UniProt10]
Alternate sequence: Q → R; UniProt: (in strain: ECOR 10);
Extrinsic-Sequence-Variant 422
[UniProt10]
Alternate sequence: S → 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;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

Chen10a: 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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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.

UniProtGOA11a: 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

Other References Related to Gene Regulation

Baker84: Baker HV, Wolf RE (1984). "Essential site for growth rate-dependent regulation within the Escherichia coli gnd structural gene." Proc Natl Acad Sci U S A 81(24);7669-73. PMID: 6440141

Hommais04: Hommais F, Krin E, Coppee JY, Lacroix C, Yeramian E, Danchin A, Bertin P (2004). "GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli." Microbiology 150(Pt 1);61-72. PMID: 14702398

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Dec 22, 2014, biocyc11.