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Escherichia coli K-12 substr. MG1655 Enzyme: L-idonate 5-dehydrogenase



Gene: idnD Accession Numbers: G7893 (EcoCyc), b4267, ECK4260

Synonyms: yjgV

Regulation Summary Diagram: ?

Summary:
L-idonate 5-dehydrogenase catalyzes the reversible oxidation of L-idonate to 5-ketogluconate. This is the first reaction of the L-idonate catabolic pathway after uptake of L-idonate into the cell. The enzyme specifically oxidizes L-idonate using NAD and catalyzes the specific reduction of 5-ketogluconate using NADH or NADPH [Bausch98].

A strain containing a deletion of idnD can not grow on L-idonate as the sole source of carbon and energy [Bausch98].

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

IdnD: "idonate" [Bausch98]

Review: [Peekhaus98a]

Locations: cytosol

Map Position: [4,491,398 <- 4,492,429] (96.8 centisomes)
Length: 1032 bp / 343 aa

Molecular Weight of Polypeptide: 37.147 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013975 , DIP:DIP-10010N , EchoBASE:EB2430 , EcoGene:EG12541 , EcoliWiki:b4267 , Mint:MINT-1242659 , ModBase:P39346 , OU-Microarray:b4267 , PortEco:idnD , PR:PRO_000022993 , Protein Model Portal:P39346 , RefSeq:NP_418688 , RegulonDB:G7893 , SMR:P39346 , String:511145.b4267 , UniProt:P39346

Relationship Links: InterPro:IN-FAMILY:IPR002085 , InterPro:IN-FAMILY:IPR011032 , InterPro:IN-FAMILY:IPR013149 , InterPro:IN-FAMILY:IPR013154 , InterPro:IN-FAMILY:IPR016040 , Panther:IN-FAMILY:PTHR11695 , Pfam:IN-FAMILY:PF00107 , Pfam:IN-FAMILY:PF08240 , Prosite:IN-FAMILY:PS00059

In Paralogous Gene Group: 103 (13 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0046183 - L-idonate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Bausch98]
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:0050572 - L-idonate 5-dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA01a, Bausch98]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for idnD knockouts: ?

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

Credits:
Last-Curated ? 15-Apr-2010 by Keseler I , SRI International


Enzymatic reaction of: L-idonate 5-dehydrogenase

EC Number: 1.1.1.264

L-idonate + 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 4]:

In Pathways: ketogluconate metabolism , L-idonate degradation

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-idonate
25000.0
[Bausch98]
5-dehydro-D-gluconate
1000.0
[Bausch98]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 40
[UniProt10a]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 65
[UniProt10a]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 93
[UniProt10a]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 96
[UniProt10a]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 99
[UniProt10a]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 107
[UniProt10a]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 153
[UniProt10a]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

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


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

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

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

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."

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

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


Report Errors or Provide Feedback
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 Sat Feb 28, 2015, biocyc12.