2pzv

From Proteopedia

Revision as of 12:56, 23 January 2008

Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol

Overview

A longstanding proposal in enzymology is that enzymes are, electrostatically and geometrically complementary to the transition states, of the reactions they catalyze and that this complementarity contributes, to catalysis. Experimental evaluation of this contribution, however, has, been difficult. We have systematically dissected the potential, contribution to catalysis from electrostatic complementarity in, ketosteroid isomerase. Phenolates, analogs of the transition state and, reaction intermediate, bind and accept two hydrogen bonds in an active, site oxyanion hole. The binding of substituted phenolates of constant, molecular shape but increasing pK(a) models the charge accumulation in the, oxyanion hole during the enzymatic reaction. As charge localization, increases, the NMR chemical shifts of protons involved in oxyanion hole, hydrogen bonds increase by 0.50-0.76 ppm/pK(a) unit, suggesting a bond, shortening of 0.02 A/pK(a) unit. Nevertheless, there is little change in, binding affinity across a series of substituted phenolates (DeltaDeltaG =, -0.2 kcal/mol/pK(a) unit). The small effect of increased charge, localization on affinity occurs despite the shortening of the hydrogen, bonds and a large favorable change in binding enthalpy (DeltaDeltaH = -2.0, kcal/mol/pK(a) unit). This shallow dependence of binding affinity suggests, that electrostatic complementarity in the oxyanion hole makes at most a, modest contribution to catalysis of 300-fold. We propose that geometrical, complementarity between the oxyanion hole hydrogen-bond donors and the, transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess, through a combination of modest contributions from several mechanisms, rather than from a single dominant contribution.

About this Structure

2PZV is a Single protein structure of sequence from Pseudomonas putida with as ligand. This structure superseeds the now removed PDB entry 2B32. Active as Steroid Delta-isomerase, with EC number 5.3.3.1 Full crystallographic information is available from OCA.

Reference

Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole., Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D, PLoS Biol. 2006 Apr;4(4):e99. Epub 2006 Mar 28. PMID:16602823

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