Role of active site binding interactions in 4-chlorobenzoyl-coenzyme A dehalogenase catalysis.
4-Chlorobenzoyl-coenzyme A (4-CBA-CoA) dehalogenase catalyzes the hydrolytic dehalogenation of 4-CBA-CoA to 4-hydroxybenzoyl-CoA (4-HBA-CoA) via a multistep mechanism involving initial attack of Asp145 on C(4) of the substrate benzoyl ring to form a Meisenheimer intermediate (EMc), followed by expulsion of the chloride ion to form an arylated enzyme intermediate (EAr) and then ester hydrolysis in the EAr to form product. This study examines the role of binding interactions in dehalogenase catalysis. The enzyme and substrate groups positioned for favorable binding interaction were identified from the X-ray crystal structure of the enzyme-4-HBA-3'-dephospho-CoA complex. These groups were individually modified (via site-directed mutagenesis or chemical synthesis) for the purpose of disrupting the binding interaction. The changes in the Gibbs free energy of the enzyme-substrate complex (DeltaDeltaG(ES)) and enzyme-transition state complex (DeltaDeltaG) brought about by the modification were measured. Cases where DeltaDeltaG exceeds DeltaDeltaG(ES) are indicative of binding interactions used for catalysis. On the basis of this analysis, we show that the H-bond interactions between the Gly114 and Phe64 backbone amide NHs and the substrate benzoyl C=O group contribute an additional 3.1 kcal/mol of stabilization at the rate-limiting transition state. The binding interactions between the enzyme and the substrate CoA nucleotide moiety also intensify in the rate-limiting transition state, reducing the energy barrier to catalysis by an additional 3.3 kcal/mol. Together, these binding interactions contribute approximately 10(6) to the k(cat)/K(m).
Luo
L
L
Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA.
Taylor
K L
KL
Xiang
H
H
Wei
Y
Y
Zhang
W
W
Dunaway-Mariano
D
D
D000214:Acyl Coenzyme A / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D001667:Binding, Competitive / Q000235:genetics; D002384:Catalysis; D003065:Coenzyme A / Q000737:chemistry / Q000378:metabolism; D004795:Enzyme Stability / Q000235:genetics; D006867:Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D008024:Ligands; D016297:Mutagenesis, Site-Directed; D010204:Pantetheine / Q000031:analogs & derivatives* / Q000378:metabolism; D013379:Substrate Specificity / Q000235:genetics; D013816:Thermodynamics
D000214:Acyl Coenzyme A; D008024:Ligands; C084334:4-chlorobenzoyl coenzyme A; C015787:dephosphocoenzyme A; D010204:Pantetheine; D006867:Hydrolases; C084333:4-chlorobenzoyl coenzyme A dehalogenase; C003129:4'-phosphopantetheine; D003065:Coenzyme A