title: The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.
abstract: We have discovered a superfamily of enzymes related by their ability to catalyze the abstraction of the alpha-proton of a carboxylic acid to form an enolic intermediate. Although each reaction catalyzed by these enzymes is initiated by this common step, their overall reactions (including racemization, beta-elimination of water, beta-elimination of ammonia, and cycloisomerization) as well as the stereochemical consequences (syn vs anti) of the beta-elimination reactions are diverse. Analysis of sequence and structural similarities among these proteins suggests that all of their chemical reactions are mediated by a common active site architecture modified through evolution to allow the enolic intermediates to partition to different products in their respective active sites via different overall mechanisms. All of these enzymes retain the ability to catalyze the thermodynamically difficult step of proton abstraction. These homologous proteins, designated the "enolase superfamily", include enolase as well as more metabolically specialized enzymes: mandelate racemase, galactonate dehydratase, glucarate dehydratase, muconate-lactonizing enzymes, N-acylamino acid racemase, beta-methylaspartate ammonia-lyase, and o-succinylbenzoate synthase. Comparative analysis of structure-function relationships within the superfamily suggests that carboxyphosphonoenolpyruvate synthase, another member of the superfamily, does not catalyze the reaction proposed in the literature but catalyzes an enolase-like reaction instead. The established and deduced structure-function relationships in the superfamily allow the prediction that other apparent members of the family for which no catalytic functions have yet been assigned will also perform chemistry involving abstraction of the alpha-protons of carboxylic acids.
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA.
authors.forename: P C
authors.initials: PC
authors.lastname: Babbitt
authors.forename: M S
authors.initials: MS
authors.lastname: Hasson
authors.forename: J E
authors.initials: JE
authors.lastname: Wedekind
authors.forename: D R
authors.initials: DR
authors.lastname: Palmer
authors.forename: W C
authors.initials: WC
authors.lastname: Barrett
authors.forename: G H
authors.initials: GH
authors.lastname: Reed
authors.forename: I
authors.initials: I
authors.lastname: Rayment
authors.forename: D
authors.initials: D
authors.lastname: Ringe
authors.forename: G L
authors.initials: GL
authors.lastname: Kenyon
authors.forename: J A
authors.initials: JA
authors.lastname: Gerlt
mesh_terms: D000595:Amino Acid Sequence; D000642:Ammonia-Lyases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D002264:Carboxylic Acids / Q000737:chemistry / Q000378:metabolism*; D002384:Catalysis; D019143:Evolution, Molecular; D006801:Humans; D019753:Intramolecular Lyases; D007535:Isomerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008670:Metals / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010751:Phosphopyruvate Hydratase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011522:Protons; D019998:Racemases and Epimerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013237:Stereoisomerism
chemical_list: D002264:Carboxylic Acids; D008670:Metals; D011522:Protons; D010751:Phosphopyruvate Hydratase; D000642:Ammonia-Lyases; C034881:methylaspartate ammonia-lyase; D007535:Isomerases; D019998:Racemases and Epimerases; C021540:mandelate racemase; D019753:Intramolecular Lyases; C021811:muconate cycloisomerase