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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.
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MetaCyc Enzyme: galactarate dehydratase

Gene: garD Accession Numbers: EG12522 (MetaCyc), b3128, ECK3116

Synonyms: yhaG

Species: Escherichia coli K-12 substr. MG1655

Summary:
Galactarate dehydratase catalyzes the dehydration of galactarate, the naturally occurring dicarboxylic acid analogue of D-galactose [Blumenthal64, Hubbard98].

Enzymatic activity of galactarate dehydratase is induced by growth on D-glucarate, galactarate, and D-glycerate [Monterrubio00].

Locations: cytosol

Map Position: [3,273,304 -> 3,274,875]

Molecular Weight of Polypeptide: 56.402 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010284 , EchoBASE:EB2413 , EcoGene:EG12522 , EcoliWiki:b3128 , OU-Microarray:b3128 , PortEco:garD , PR:PRO_000022750 , Pride:P39829 , Protein Model Portal:P39829 , RefSeq:NP_417597 , RegulonDB:EG12522 , SMR:P39829 , String:511145.b3128 , UniProt:P39829

Relationship Links: InterPro:IN-FAMILY:IPR007392 , InterPro:IN-FAMILY:IPR013974 , InterPro:IN-FAMILY:IPR017654 , PDB:Structure:3LAZ , Pfam:IN-FAMILY:PF04295 , Pfam:IN-FAMILY:PF08666 , Smart:IN-FAMILY:SM00858

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0046392 - galactarate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA01a, Hubbard98]
Molecular Function: GO:0008867 - galactarate dehydratase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Hubbard98]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016836 - hydro-lyase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

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


Enzymatic reaction of: galactarate dehydratase

Synonyms: galactarate dehydrase, D-galactarate hydro-lyase, GalcD

EC Number: 4.2.1.42

D-galactarate <=> 5-dehydro-4-deoxy-D-glucarate + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of D-glucarate and D-galactarate degradation , superpathway of microbial D-galacturonate and D-glucuronate degradation , D-galactarate degradation I

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

Summary:
Galactarate dehydratase is catalytically inactive in the absence of Fe2+, Mn2+ and β-mercaptoethanol; however, under certain conditios, the enzyme is inhibited by Mn2+ [Hubbard98].

The enzyme was originally isolated from E. coli strain CR63MA, but is present in other strains including K-12 [Blumenthal64].

Cofactors or Prosthetic Groups [Comment 1]: Fe2+ [Hubbard98]

Activators (Unknown Mechanism): 2-mercaptoethanol [Hubbard98]

Inhibitors (Unknown Mechanism): cacodylate [Blumenthal66] , phosphate [Blumenthal66] , citrate [Blumenthal66] , potassium cyanide [Blumenthal66, Blumenthal64] , diphosphate [Blumenthal66, Blumenthal64]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
D-galactarate
800.0
22.0
[Hubbard98, BRENDA14]

pH(opt): 7.5 [Hubbard98]

History:
10/20/97 Gene b3128 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12522; confirmed by SwissProt match.


References

Blumenthal64: Blumenthal HJ, Jepson T (1964). "Asymmetric dehydration of galactarate by bacterial galactarate dehydratase." Biochem Biophys Res Commun 1964;17(3);282-7. PMID: 4285952

Blumenthal66: Blumenthal, HJ, Jepson, T "Galactarate Dehydrase." Methods in Enzymology 9:665-669 (1966).

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Hubbard98: Hubbard BK, Koch M, Palmer DR, Babbitt PC, Gerlt JA (1998). "Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli." Biochemistry 1998;37(41);14369-75. PMID: 9772162

Monterrubio00: Monterrubio R, Baldoma L, Obradors N, Aguilar J, Badia J (2000). "A common regulator for the operons encoding the enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization in Escherichia coli." J Bacteriol 2000;182(9);2672-4. PMID: 10762278

UniProtGOA11a: 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."


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 Sat Dec 20, 2014, biocyc11.