MetaCyc Enzyme: α-dehydro-β-deoxy-D-glucarate aldolase

Gene: garL Accession Numbers: EG10016 (MetaCyc), b3126, ECK3114

Synonyms: yhaF

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of α-dehydro-β-deoxy-D-glucarate aldolase = [GarL]6

α-dehydro-β-deoxy-D-glucarate aldolase cleaves both 5-dehydro-4-deoxy- and 2-dehydro-3-deoxy-D-glucarate, thereby continuing the catabolism of D-glucarate and D-galactarate [Fish66, Hubbard98].

Crystal structures of the enzyme alone and in complex with pyruvate have been solved. The enzyme is a hexamer that may be assembled by association of three dimers [Blackwell99, Izard00].

Locations: cytosol

Map Position: [3,270,809 <- 3,271,579]

Molecular Weight of Polypeptide: 27.384 kD (from nucleotide sequence), 27.4 kD (experimental) [Blackwell99 ]

Unification Links: ASAP:ABE-0010276 , DIP:DIP-9740N , EchoBASE:EB0016 , EcoGene:EG10016 , EcoliWiki:b3126 , ModBase:P23522 , OU-Microarray:b3126 , PortEco:garL , PR:PRO_000022752 , Pride:P23522 , Protein Model Portal:P23522 , RefSeq:NP_417595 , RegulonDB:EG10016 , SMR:P23522 , String:511145.b3126 , UniProt:P23522

Relationship Links: InterPro:IN-FAMILY:IPR005000 , InterPro:IN-FAMILY:IPR015813 , InterPro:IN-FAMILY:IPR017648 , PDB:Structure:1DXE , PDB:Structure:1DXF , Pfam:IN-FAMILY:PF03328

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0019394 - glucarate catabolic process Inferred from experiment [Hubbard98]
GO:0042838 - D-glucarate catabolic process Inferred from experiment Inferred by computational analysis [GOA06, Hubbard98]
GO:0046392 - galactarate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA06, Hubbard98]
Molecular Function: GO:0008672 - 2-dehydro-3-deoxyglucarate aldolase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Hubbard98, Fish66]
GO:0016830 - carbon-carbon lyase activity Inferred from experiment [Hubbard98]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Hubbard98]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Created in EcoCyc 21-Aug-2007 by Keseler I , SRI International
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Enzymatic reaction of: α-dehydro-β-deoxy-D-glucarate aldolase

Synonyms: KDG aldolase, 2-dehydro-3-deoxyglucarate aldolase, 2-keto-3-deoxyglucarate aldolase, 2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase, 5-dehydro-4-deoxy-D-glucarate aldolase, ketodeoxyglucarate aldolase, KDGlucA

5-dehydro-4-deoxy-D-glucarate <=> pyruvate + tartronate semialdehyde

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.

Alternative Substrates for 5-dehydro-4-deoxy-D-glucarate: (2S,3S)-2,3-dihydroxy-5-oxohexanedioate

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

Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

The enzyme was first isolated from E. coli strain CR63MA but is known to occur in other strains including K-12 [Fish66, Roberton80].

The equilibrium constant lies far in the direction of cleavage [Fish66].

Cofactors or Prosthetic Groups: Mg2+ [Comment 1, Fish66]

Inhibitors (Competitive): 2-dehydro-3-deoxy-D-gluconate 6-phosphate [Fish66] , 3-deoxy-D-manno-octulosonate [Fish66] , 2-keto-D-gluconate [Fish66]

Inhibitors (Other): ketodeoxyheptonate [Fish66] , a xylarate [Fish66] , D-glucarate [Fish66, Comment 2] , galactarate [Fish66, Comment 2]

Inhibitors (Unknown Mechanism): a tetrarate [Fish66] , a hexonic acid [Fish66] , a pentaric acid [Fish66] , a hexuronate [Fish66] , a hexaric acid [Fish66] , acetate [Fish66] , chloride [Fish66] , nitrate [Fish66] , bromide [Fish66] , fluoride [Fish66] , EDTA [Fish66] , diphosphate [Fish66] , hydrogen cyanide [Fish66]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
0.065, 65.0
420.0, 0.42
[Hubbard98, BRENDA14]

pH(opt): 8 [BRENDA14, Rea08]

Sequence Features

Feature Class Location Citations Comment
Active-Site 50
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 75
UniProt: Transition state stabilizer; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 89
UniProt: Increases basicity of active site His; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 151
UniProt: Substrate.
Metal-Binding-Site 153
UniProt: Magnesium.
Amino-Acid-Sites-That-Bind 178
UniProt: Substrate; via amide nitrogen.
Metal-Binding-Site 179
UniProt: Magnesium.

10/20/97 Gene b3126 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10016; confirmed by SwissProt match.


Blackwell99: Blackwell NC, Cullis PM, Cooper RA, Izard T (1999). "Rhombohedral crystals of 2-dehydro-3-deoxygalactarate aldolase from Escherichia coli." Acta Crystallogr D Biol Crystallogr 55(Pt 7);1368-9. PMID: 10393309

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

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

Fish66: Fish D, Blumenthal H "2-keto-3-deoxy-D-glucarate aldolase." Meth Enz 1966;9:529-534.

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.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Izard00: Izard T, Blackwell NC (2000). "Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism." EMBO J 19(15);3849-56. PMID: 10921867

Rea08: Rea D, Hovington R, Rakus JF, Gerlt JA, Fulop V, Bugg TD, Roper DI (2008). "Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12." Biochemistry 47(38);9955-65. PMID: 18754683

Roberton80: Roberton AM, Sullivan PA, Jones-Mortimer MC, Kornberg HL (1980). "Two genes affecting glucarate utilization in Escherichia coli K12." J Gen Microbiol 1980;117(2);377-82. PMID: 6999115

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

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 19.0 on Tue Jul 28, 2015, biocyc14.