Testing geometrical discrimination within an enzyme active site: Constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole

Paul A. Sigala, Daniel Kraut, Jose M.M. Caaveiro, Brandon Pybus, Eliza Ruben, Dagmar Ringe, Gregory A. Petsko, Daniel Herschlag

Research output: Contribution to journalArticle

80 Citations (Scopus)

Abstract

Enzymes are classically proposed to accelerate reactions by binding substrates within active- site environments that are structurally preorganized to optimize binding interactions with reaction transition states rather than ground states. This is a remarkably formidable task considering the limited 0.1-1 Å scale of most substrate rearrangements. The flexibility of active-site functional groups along the coordinate of substrate rearrangement, the distance scale on which enzymes can distinguish structural rearrangement, and the energetic significance of discrimination on that scale remain open questions that are fundamental to a basic physical understanding of enzyme active sites and catalysis. We bring together 1.2-1.5 Å resolution X-ray crystallography, 1H and 19F NMR spectroscopy, quantum mechanical calculations, and transition-state analogue binding measurements to test the distance scale on which noncovalent forces can constrain the structural relaxation or translation of side chains and ligands along a specific coordinate and the energetic consequences of such geometric constraints within the active site of bacterial ketosteroid isomerase (KSI). Our results strongly suggest that packing and binding interactions within the KSI active site can constrain local side-chain reorientation and prevent hydrogen bond shortening by 0.1 Å or less. Further, this constraint has substantial energetic effects on ligand binding and stabilization of negative charge within the oxyanion hole. These results provide evidence that subtle geometric effects, indistinguishable in most X-ray crystallographic structures, can have significant energetic consequences and highlight the importance of using synergistic experimental approaches to dissect enzyme function.
Original languageEnglish
Pages (from-to)13696-13708
Number of pages13
JournalJournal of the American Chemical Society
Volume130
DOIs
Publication statusPublished - 2008

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Ketosteroids
Isomerases
Hydrogen Bonding
Catalytic Domain
Hydrogen bonds
Enzymes
Testing
Substrates
Ligands
Structural relaxation
X ray crystallography
Electron transitions
Ground state
Functional groups
Catalysis
Nuclear magnetic resonance spectroscopy
X Ray Crystallography
Stabilization
Hydrogen
X rays

Cite this

Testing geometrical discrimination within an enzyme active site: Constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. / Sigala, Paul A.; Kraut, Daniel; Caaveiro, Jose M.M.; Pybus, Brandon; Ruben, Eliza; Ringe, Dagmar; Petsko, Gregory A.; Herschlag, Daniel.

In: Journal of the American Chemical Society, Vol. 130, 2008, p. 13696-13708.

Research output: Contribution to journalArticle

Sigala, Paul A. ; Kraut, Daniel ; Caaveiro, Jose M.M. ; Pybus, Brandon ; Ruben, Eliza ; Ringe, Dagmar ; Petsko, Gregory A. ; Herschlag, Daniel. / Testing geometrical discrimination within an enzyme active site: Constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. In: Journal of the American Chemical Society. 2008 ; Vol. 130. pp. 13696-13708.
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AB - Enzymes are classically proposed to accelerate reactions by binding substrates within active- site environments that are structurally preorganized to optimize binding interactions with reaction transition states rather than ground states. This is a remarkably formidable task considering the limited 0.1-1 Å scale of most substrate rearrangements. The flexibility of active-site functional groups along the coordinate of substrate rearrangement, the distance scale on which enzymes can distinguish structural rearrangement, and the energetic significance of discrimination on that scale remain open questions that are fundamental to a basic physical understanding of enzyme active sites and catalysis. We bring together 1.2-1.5 Å resolution X-ray crystallography, 1H and 19F NMR spectroscopy, quantum mechanical calculations, and transition-state analogue binding measurements to test the distance scale on which noncovalent forces can constrain the structural relaxation or translation of side chains and ligands along a specific coordinate and the energetic consequences of such geometric constraints within the active site of bacterial ketosteroid isomerase (KSI). Our results strongly suggest that packing and binding interactions within the KSI active site can constrain local side-chain reorientation and prevent hydrogen bond shortening by 0.1 Å or less. Further, this constraint has substantial energetic effects on ligand binding and stabilization of negative charge within the oxyanion hole. These results provide evidence that subtle geometric effects, indistinguishable in most X-ray crystallographic structures, can have significant energetic consequences and highlight the importance of using synergistic experimental approaches to dissect enzyme function.

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