Escherichia coli K-12 substr. MG1655 Polypeptide: glycolate oxidase, predicted iron-sulfur subunit

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

Synonyms: gox, yghL, b2978 (obsolete)

Regulation Summary Diagram: ?

Regulation summary diagram for glcF

Component of: glycolate oxidase (summary available)

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

Gene Citations: [Nunez01a]

Locations: cytosol, inner membrane

Map Position: [3,122,258 <- 3,123,481] (67.29 centisomes, 242°)
Length: 1224 bp / 407 aa

Molecular Weight of Polypeptide: 45.11 kD (from nucleotide sequence), 45 kD (experimental) [Pellicer96 ]

Unification Links: ASAP:ABE-0174097 , EchoBASE:EB3076 , EcoGene:EG13291 , EcoliWiki:b4467 , ModBase:P52074 , PortEco:glcF , Pride:P52074 , Protein Model Portal:P52074 , RefSeq:YP_026190 , RegulonDB:G0-8601 , SMR:P52074 , String:511145.b4467 , UniProt:P52074

Relationship Links: InterPro:IN-FAMILY:IPR004017 , InterPro:IN-FAMILY:IPR012257 , InterPro:IN-FAMILY:IPR017896 , InterPro:IN-FAMILY:IPR017900 , OU-Microarray:RELATED-TO:b2978 , Pfam:IN-FAMILY:PF02754 , Pfam:IN-FAMILY:PF13183 , Prosite:IN-FAMILY:PS00198 , Prosite:IN-FAMILY:PS51379

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for glcF

GO Terms:

Biological Process: GO:0046296 - glycolate catabolic process Inferred from experiment [Pellicer96]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0019154 - glycolate dehydrogenase activity Inferred from experiment [Pellicer96]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005886 - plasma membrane [Pellicer96]

MultiFun Terms: metabolism central intermediary metabolism glycolate metabolism

Essentiality data for glcF 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 ? 30-Nov-2006 by Keseler I , SRI International

Subunit of: glycolate oxidase

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)

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].

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

Enzymatic reaction of: glycolate oxidase

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

EC Number:

glycolate + an oxidized unknown electron acceptor <=> glyoxylate + an reduced unknown electron acceptor

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.

Alternative Substrates for glycolate [Lord72 ]: (R)-lactate [Comment 5 , Lord72 ]

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

Inhibitors (Unknown Mechanism): Zn2+ [Lord72] , copper sulfate [Lord72] , p-chloromercuribenzoate [Lord72] , Hg2+ [Lord72] , potassium cyanide [Lord72]

Kinetic Parameters:

Km (μM)

pH(opt): 8-8.8 [Lord72]

Sequence Features

Protein sequence of glycolate oxidase, predicted iron-sulfur subunit with features indicated

Feature Class Location Citations Comment
Conserved-Region 14 -> 47
UniProt: 4Fe-4S ferredoxin-type 1;
Metal-Binding-Site 25
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 28
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 31
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 35
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 66 -> 95
UniProt: 4Fe-4S ferredoxin-type 2;
Metal-Binding-Site 75
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 78
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 81
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 85
UniProt: Iron-sulfur 1 (4Fe-4S); 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



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

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

Nunez01a: Nunez MF, Pellicer MT, Badia J, Aguilar J, Baldoma L (2001). "The gene yghK linked to the glc operon of Escherichia coli encodes a permease for glycolate that is structurally and functionally similar to L-lactate permease." Microbiology 2001;147(Pt 4);1069-77. PMID: 11283302

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

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

Other References Related to Gene Regulation

Gohler11: Gohler AK, Kokpinar O, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C (2011). "More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli." BMC Syst Biol 5(1);197. PMID: 22168595

Liu04d: Liu X, De Wulf P (2004). "Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling." J Biol Chem 279(13);12588-97. PMID: 14711822

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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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