Observation of Covalent Intermediates in an Enzyme Mechanism at Atomic Resolution

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Science  12 Oct 2001:
Vol. 294, Issue 5541, pp. 369-374
DOI: 10.1126/science.1063601

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In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra–high resolution structures of wild-type and mutantd-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and Schiff base intermediates in the aldolase mechanism. In combination with site-directed mutagenesis and1H nuclear magnetic resonance, we can now propose how the heretofore elusive C-2 proton abstraction step and the overall stereochemical course are accomplished. A proton relay system appears to activate a conserved active-site water that functions as the critical mediator for proton transfer.

  • * These authors contributed equally to this work.

  • Present address: Diversa Corporation, 4955 Directors Place, San Diego, CA 92121, USA.

  • To whom correspondence should be addressed. E-mail: wong{at} (C.-H.W.); wilson{at} (I.A.W.)

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