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.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

MetaCyc Polypeptide: glycolate oxidase, predicted iron-sulfur subunit

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

Synonyms: gox, yghL, b2978 (obsolete)

Species: Escherichia coli K-12 substr. MG1655

Component of: glycolate oxidase (summary available)

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

Locations: cytosol, inner membrane

Map Position: [3,122,258 <- 3,123,481]

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:IPR012285 , 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: ?

GO Terms:

Biological Process: GO:0046296 - glycolate catabolic process Inferred from experiment [Pellicer96]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0019154 - glycolate dehydrogenase activity Inferred from experiment [Pellicer96]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005886 - plasma membrane [Pellicer96]

MultiFun Terms: metabolism central intermediary metabolism glycolate metabolism

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


Subunit of: glycolate oxidase

Species: Escherichia coli K-12 substr. MG1655

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].

Credits:
Created in EcoCyc 30-Nov-2006 by Keseler I , SRI International
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: glycolate oxidase

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

EC Number: 1.1.99.14

glycolate + an oxidized electron acceptor <=> glyoxylate + a reduced 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 1 , Lord72 ]

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

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

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]


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 14 -> 47
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 1;
Metal-Binding-Site 25
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 28
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 31
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 35
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 66 -> 95
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 2;
Metal-Binding-Site 75
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 78
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 81
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 85
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;


References

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."

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

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

UniProt10: 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."


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 Sun Dec 21, 2014, BIOCYC13B.