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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
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MetaCyc Enzyme: 5-keto-D-gluconate 5-reductase

Gene: idnO Accession Numbers: G7892 (MetaCyc), b4266, ECK4259

Synonyms: yjgU

Species: Escherichia coli K-12 substr. MG1655

Summary:
5-Keto-D-gluconate 5-reductase catalyzes the reversible reduction of 5-ketogluconate to D-gluconate. This is the second reaction of the L-idonate catabolic pathway after uptake of L-idonate into the cell. The enzyme specifically reduces 5-ketogluconate using either NADH or NADPH. D-gluconate oxidation by the enzyme can only proceed with NAD as the coenzyme; NADP only results in low specific activity [Bausch98].

Based on sequence similarity, IdnO was predicted to be an acetoin dehydrogenase (diacetyl reductase) [Reed03].

Expression of the idnDOTR operon is catabolite repressed and induced by L-idonate or 5-ketogluconate [Bausch04].

IdnO: "idonate" [Bausch98]

Review: [Peekhaus98]

Locations: cytosol

Map Position: [4,490,610 <- 4,491,374]

Molecular Weight of Polypeptide: 27.563 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013971 , EchoBASE:EB2429 , EcoGene:EG12540 , EcoliWiki:b4266 , Mint:MINT-1231433 , ModBase:P0A9P9 , OU-Microarray:b4266 , PortEco:idnO , PR:PRO_000022995 , Protein Model Portal:P0A9P9 , RefSeq:NP_418687 , RegulonDB:G7892 , SMR:P0A9P9 , String:511145.b4266 , UniProt:P0A9P9

Relationship Links: EcoO157Cyc:Homolog:Z1533 , EcoO157Cyc:Homolog:Z1533-MONOMER , InterPro:IN-FAMILY:IPR002198 , InterPro:IN-FAMILY:IPR002347 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR020904 , Pfam:IN-FAMILY:PF00106 , Prints:IN-FAMILY:PR00080 , Prints:IN-FAMILY:PR00081 , Prosite:IN-FAMILY:PS00061

Gene-Reaction Schematic: ?

Instance reactions of [D-gluconate + NAD(P)+ ↔ 5-dehydro-D-gluconate + NAD(P)H + H+] (1.1.1.69):
i1: D-gluconate + NAD+ ↔ 5-dehydro-D-gluconate + NADH + H+ (no EC#)

i2: D-gluconate + NADP+ ← 5-dehydro-D-gluconate + NADPH + H+ (1.1.1.-)

GO Terms:

Biological Process: GO:0046183 - L-idonate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Bausch98]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0019521 - D-gluconate metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0008874 - gluconate 5-dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA01a, Yum99, Bausch98]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

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


Enzymatic reaction of: 5-keto-D-gluconate 5-reductase

Synonyms: gluconate 5-dehydrogenase, D-gluconate:NAD(P)+ 5-oxidoreductase, 5KDGR

EC Number: 1.1.1.69

D-gluconate + NAD(P)+ <=> 5-dehydro-D-gluconate + NAD(P)H + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Bausch98]

Alternative Substrates [Comment 1]:

In Pathways: ketogluconate metabolism , L-idonate degradation

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

Summary:
The specific activity of the enzyme in the 5-keto-D-gluconate 5-reductase direction is more than 10-fold higher than in the oxidation direction [Bausch98]. Although the enzyme can utilize both NADH and NADPH, it has three times the activity using NADH [Yum99].

Kinetic Parameters:

Substrate
Km (μM)
Citations
5-dehydro-D-gluconate
500.0
[Bausch98]
D-gluconate
2000.0
[Bausch98]

pH(opt) (reverse direction): 8.0 [Yum99]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 13 -> 37
[UniProt10a]
UniProt: NADP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 145
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Active-Site 158
[UniProt10a]
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Bausch04: Bausch C, Ramsey M, Conway T (2004). "Transcriptional organization and regulation of the L-idonic acid pathway (GntII system) in Escherichia coli." J Bacteriol 186(5);1388-97. PMID: 14973046

Bausch98: Bausch C, Peekhaus N, Utz C, Blais T, Murray E, Lowary T, Conway T (1998). "Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli." J Bacteriol 1998;180(14);3704-10. PMID: 9658018

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

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.

Peekhaus98: Peekhaus N, Conway T (1998). "What's for dinner?: Entner-Doudoroff metabolism in Escherichia coli." J Bacteriol 1998;180(14);3495-502. PMID: 9657988

Reed03: Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)." Genome Biol 4(9);R54. PMID: 12952533

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Yum99: Yum DY, Lee BY, Pan JG (1999). "Identification of the yqhE and yafB genes encoding two 2, 5-diketo-D-gluconate reductases in Escherichia coli." Appl Environ Microbiol 1999;65(8);3341-6. PMID: 10427017


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 Mon Dec 22, 2014, biocyc13.