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Escherichia coli K-12 substr. MG1655 Enzyme: glycolate oxidase
Inferred from experiment


Subunit composition of glycolate oxidase = [GlcD][GlcE][GlcF]
         glycolate oxidase, predicted FAD-linked subunit = GlcD
         glycolate oxidase, predicted FAD-binding subunit = GlcE
         glycolate oxidase, predicted iron-sulfur subunit = GlcF (summary available)

Summary:
Glycolate oxidase catalyzes the first step in the utilization of glycolate as the sole source of carbon [Lord72]. The enzyme may be membrane-associated; Sallal and Nimer ( [Sallal89]) isolated a cytoplasmic membrane-associated glycolate oxidoreductase activity from E. coli ATCC11775 (serovar O1:K1:H7), and the GlcF subunit itself could only be detected in the membrane fraction [Pellicer96]. The physiological electron acceptor is unknown.

Crude extracts from an E. coli strain expressing glcDEF from a multicopy plasmid contain glycolate oxidase activity. Insertion mutants in either glcD, glcE, or glcF abolish this activity, suggesting that all three gene products are subunits of a glycolate oxidase complex [Pellicer96].

Expression of the glcDEFGB operon is induced by growth on glycolate [Pellicer99].

Gene-Reaction Schematic

Gene-Reaction Schematic

Credits:
Created 30-Nov-2006 by Keseler I, SRI International
Last-Curated 24-Aug-2007 by Keseler I, SRI International


Enzymatic reaction of: glycolate oxidase

Inferred from experiment

Synonyms: glycolate oxidoreductase, glycolate:(acceptor) 2-oxidoreductase, glycolate dehydrogenase

EC Number: 1.1.99.14

glycolate + an oxidized unknown electron acceptor → glyoxylate + an reduced unknown electron acceptor

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for glycolate [Lord72]: (R)-lactate [Comment 1, Lord72]

In Pathways: superpathway of glycol metabolism and degradation, glycolate and glyoxylate degradation II, glycolate and glyoxylate degradation I

Inhibitors (Unknown Mechanism): Zn2+ [Lord72], copper sulfate [Lord72], p-chloromercuribenzoate [Lord72], Hg2+ [Lord72], potassium cyanide [Lord72]Kinetic Parameters:
Substrate Km (μM) Citations
glycolate 40.0 [Lord72]

pH(opt): 8-8.8 [Lord72]


Subunit of glycolate oxidase: glycolate oxidase, predicted FAD-linked subunit

Synonyms: YghM, Gox, GlcD

Gene: glcD Accession Numbers: G7545 (EcoCyc), b2979, ECK2974

Locations: cytosol

Sequence Length: 499 AAs

Molecular Weight: 53.812 kD (from nucleotide sequence)

Molecular Weight: 56 kD (experimental) [Pellicer96]


GO Terms:
Biological Process:
Inferred from experimentGO:0006974 - cellular response to DNA damage stimulus [Khil02]
Inferred from experimentGO:0046296 - glycolate catabolic process [Pellicer96]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred from experimentGO:0019154 - glycolate dehydrogenase activity [Pellicer96]
Inferred by computational analysisGO:0003824 - catalytic activity [GOA01a]
Inferred by computational analysisGO:0008891 - glycolate oxidase activity [GOA01a]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [GOA01a]
Inferred by computational analysisGO:0050660 - flavin adenine dinucleotide binding [GOA01a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]
Inferred by computational analysisGO:0009339 - glycolate oxidase complex [GOA01a]

MultiFun Terms: metabolismcentral intermediary metabolismglycolate metabolism

Unification Links: EcoliWiki:b2979, ModBase:P0AEP9, Protein Model Portal:P0AEP9, RefSeq:NP_417453, SMR:P0AEP9, UniProt:P0AEP9

Relationship Links: InterPro:IN-FAMILY:IPR004113, InterPro:IN-FAMILY:IPR004490, InterPro:IN-FAMILY:IPR006094, InterPro:IN-FAMILY:IPR016164, InterPro:IN-FAMILY:IPR016166, InterPro:IN-FAMILY:IPR016167, InterPro:IN-FAMILY:IPR016169, InterPro:IN-FAMILY:IPR016171, Pfam:IN-FAMILY:PF01565, Pfam:IN-FAMILY:PF02913, Prosite:IN-FAMILY:PS51387

Essentiality data for glcD knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 2]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]
Yes [Feist07, Comment 5]

Subunit of glycolate oxidase: glycolate oxidase, predicted FAD-binding subunit

Synonyms: Gox, YghL, GlcE

Gene: glcE Accession Numbers: G7544 (EcoCyc), b4468, ECK2973

Sequence Length: 350 AAs

Molecular Weight: 38.361 kD (from nucleotide sequence)

Molecular Weight: 40 kD (experimental) [Pellicer96]


GO Terms:
Biological Process:
Inferred from experimentGO:0046296 - glycolate catabolic process [Pellicer96]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred from experimentGO:0019154 - glycolate dehydrogenase activity [Pellicer96]
Inferred by computational analysisGO:0003824 - catalytic activity [GOA01a]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [GOA01a]
Inferred by computational analysisGO:0050660 - flavin adenine dinucleotide binding [GOA01a]

MultiFun Terms: metabolismcentral intermediary metabolismglycolate metabolism

Unification Links: EcoliWiki:b4468, ModBase:P52073, Protein Model Portal:P52073, RefSeq:YP_026191, SMR:P52073, UniProt:P52073

Relationship Links: InterPro:IN-FAMILY:IPR006094, InterPro:IN-FAMILY:IPR016164, InterPro:IN-FAMILY:IPR016166, InterPro:IN-FAMILY:IPR016169, InterPro:IN-FAMILY:IPR016171, Pfam:IN-FAMILY:PF01565, Prosite:IN-FAMILY:PS51387

Essentiality data for glcE knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]
Yes [Feist07, Comment 5]

Subunit of glycolate oxidase: glycolate oxidase, predicted iron-sulfur subunit

Synonyms: YghL, Gox, GlcF

Gene: glcF Accession Numbers: G0-8601 (EcoCyc), b4467, ECK2972

Locations: cytosol, inner membrane

Sequence Length: 407 AAs

Molecular Weight: 45.11 kD (from nucleotide sequence)

Molecular Weight: 45 kD (experimental) [Pellicer96]


GO Terms:
Biological Process:
Inferred from experimentGO:0046296 - glycolate catabolic process [Pellicer96]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0019154 - glycolate dehydrogenase activity [Pellicer96]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]
GO:0005886 - plasma membrane [Pellicer96]

MultiFun Terms: metabolismcentral intermediary metabolismglycolate metabolism

Unification Links: EcoliWiki:b4467, ModBase:P52074, Pride:P52074, Protein Model Portal:P52074, RefSeq:YP_026190, SMR:P52074, UniProt:P52074

Relationship Links: InterPro:IN-FAMILY:IPR004017, InterPro:IN-FAMILY:IPR012257, InterPro:IN-FAMILY:IPR017896, InterPro:IN-FAMILY:IPR017900, Pfam:IN-FAMILY:PF02754, Pfam:IN-FAMILY:PF13183, Prosite:IN-FAMILY:PS00198, Prosite:IN-FAMILY:PS51379

Summary:
GlcF could only be detected as a membrane-associated protein [Pellicer96].

Essentiality data for glcF knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 2]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]
Yes [Feist07, Comment 5]

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

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

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

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Lord72: Lord JM (1972). "Glycolate oxidoreductase in Escherichia coli." Biochim Biophys Acta 1972;267(2);227-37. PMID: 4557653

Pellicer96: Pellicer MT, Badia J, Aguilar J, Baldoma L (1996). "glc locus of Escherichia coli: characterization of genes encoding the subunits of glycolate oxidase and the glc regulator protein." J Bacteriol 1996;178(7);2051-9. PMID: 8606183

Pellicer99: Pellicer MT, Fernandez C, Badia J, Aguilar J, Lin EC, Baldom L (1999). "Cross-induction of glc and ace operons of Escherichia coli attributable to pathway intersection. Characterization of the glc promoter." J Biol Chem 274(3);1745-52. PMID: 9880556

Sallal89: Sallal AK, Nimer NA (1989). "The intracellular localization of glycolate oxidoreductase in Escherichia coli." FEBS Lett 1989;258(2);277-80. PMID: 2689218

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


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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