Escherichia coli K-12 substr. MG1655 Enzyme: 5-keto-D-gluconate 5-reductase

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

Synonyms: yjgU

Regulation Summary Diagram: ?

Regulation summary diagram for idnO

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: [Peekhaus98a]

Locations: cytosol

Map Position: [4,490,610 <- 4,491,374] (96.79 centisomes, 348°)
Length: 765 bp / 254 aa

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: ?

Gene-Reaction Schematic

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

Genetic Regulation Schematic: ?

Genetic regulation schematic for idnO

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

Essentiality data for idnO 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]

Last-Curated ? 06-Nov-2012 by Keseler I , SRI International

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

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

EC Number:

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 5]:

In Pathways: ketogluconate metabolism , L-idonate degradation

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:

Km (μM)

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

Sequence Features

Protein sequence of 5-keto-D-gluconate 5-reductase with features indicated

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

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


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


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

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

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

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, 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.

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

Peekhaus98a: 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

Other References Related to Gene Regulation

Rodionov00: Rodionov DA, Mironov AA, Rakhmaninova AB, Gelfand MS (2000). "Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria." Mol Microbiol 38(4);673-83. PMID: 11115104

Tsunedomi03a: Tsunedomi R, Izu H, Kawai T, Yamada M (2003). "Dual control by regulators, GntH and GntR, of the GntII genes for gluconate metabolism in Escherichia coli." J Mol Microbiol Biotechnol 6(1);41-56. PMID: 14593252

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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 19.0 on Thu Oct 8, 2015, biocyc13.