Structure of Hexadienoyl-CoA Bound to Enoyl-CoA Hydratase Determined by Transferred Nuclear Overhauser Effect Measurements: Mechanistic Predictions Based on the X-ray Structure of 4-(Chlorobenzoyl)-CoA Dehalogenase

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Abstract
The structure of the substrate analog 2,4-hexadienoyl-coenzyme A (HD-CoA) bound to the enzyme enoyl-CoA hydratase has been determined using transferred nuclear Overhauser enhancement (TRNOE) spectroscopy. NOEs between the adenine H8 proton and several pantetheine protons in the bound form of HD-CoA indicate that the overall structure of the CoA molecule is bent, while NOEs between adenine and ribose protons indicate that the conformation about the glycosidic bond is anti. The absence of long range NOEs along the pantetheine moiety is consistent with this region of the molecule being bound in an extended conformation. In addition, NOEs between the vinylic protons indicate that the HD moiety is s-trans about C3−C4. The conformation of the CoA portion of bound HD-CoA is strikingly similar to that of the CoA portion of 4-(hydroxybenzoyl)-CoA bound to the active site of 4-(chlorobenzoyl)-CoA dehalogenase [Benning, M. M., et al. (1996) Biochemistry 35, 8103−8109]. The structural similarity of the ligands along with the primary sequence homology validates the modeling of the enoyl-CoA hydratase structure with the 4-(chlorobenzoyl)-CoA dehalogenase backbone. The homology modeling allows the prediction that the enoyl-CoA substrates are bound in an s-cis conformation about C1−C2 and that Glu 144 is present at the active site and can function as a general acid/base.