Structural Basis of Perturbed Pka Values of Catalytic Groups in Enzyme Active Sites

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Life, 53: 85–98, 2002 Copyright c 2002 IUBMB 1521-6543/02 $12.00 + .00 DOI: 10.1080/10399710290038972

Review Article
Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites Thomas K. Harris1 and George J. Turner2
Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, Florida 2 Department of Physiology and Biophysics and the Neurosciences Program, University of Miami School of Medicine, Miami, Florida 1

Summary In protein and RNA macromolecules, only a limited number of different side-chain chemical groups are available to function as catalysts. The myriad of enzyme-catalyzed reactions results from the ability of most of these groups to function either as nucleophilic, electrophilic, or general acid–base catalysts, and the key to their adapted chemical function lies in their states of protonation. Ionization is determined by the intrinsic pKa of the group and the microenvironment created around the group by the protein or RNA structure, which perturbs its intrinsic pKa to its functional or apparent pKa . These pKa shifts result from interactions of the catalytic group with other fully or partially charged groups as well as the polarity or dielectric of the medium that surrounds it. The electroReceived 26 November 2001; accepted 28 January 2002. Address correspondence to Thomas K. Harris, University of Miami School of Medicine, Department of Biochemistry and Molecular Biology (R-629), P. O. Box 016129, Miami, FL 33101-6129, USA. Fax: 305-243-3955. E-mail:

static interactions between ionizable groups found on the surface of macromolecules are weak and cause only slight pKa perturbations (2 units) and are the subject of this review. The magnitudes of these pKa perturbations are analyzed with respect to the structural details of the active-site microenvironment and the energetics of the reactions that they catalyze. IUBMB Life, 53: 85–98, 2002 Keywords Acetoacetate decarboxylase; bacteriorhodopsin; cysteine protease; glycosidase; serine protease; thioredoxin.

Abbreviations: AAD, acetoacetate decarboxylase; AbAld, antibody aldolase; Ala-Race, alanine racemase; hdvAR, hepatitis delta virus antigenomic ribozyme; ArsC, arsenate reductase; AspAT, aspartate aminotransferase; BCX, Bacillus circulans xylanase; BR, ground-state bacteriorhodopsin with all trans retinal, protonated D96, protonated Schiff base, and unprotonated D85; BR-M, excited M-state bacteriorhodopsin with 13-cis retinal, protonated D96, unprotonated Schiff base, and protonated D85; BR-N, excited N-state bacteriorhodopsin with 13-cis retinal, unprotonated D96, protonated Schiff base, and protonated D85; Chy-TFKs, chymotrypsin complexed with various peptidyl trifluoro etones; hmCK, human muscle creatine kinase; DsbA and DsbC, disulfid bond enzymes A and C in E. coli; GalE, UDP-galactose 4-epimerase; GRX, glutaredoxin; HB, hydrogen bond; HPE, hydrophobic environment; KSI, ketosteroid isomerase; LBHB, low-barrier hydrogen bond; NMR, nuclear magnetic resonance; NTα, N-terminus of an α-helix; Nuc/Lv, nucleophile/leaving group; 4-OT, 4-oxalocrotonate tautomerase; PDI, protein disulfid isomerase; PLP, pyridoxal 5 -phosphate; PMP, pyridoxamine 5 -phosphate; blmPTP, bovine liver low molecular weight protein tyrosine phosphatase; hPTP1, human protein tyrosine phosphatase; yPTP, Yersenia protein tyrosine phosphatase; rPTC, ribosomal peptidyl transferase center; RNaseH1, ribonuclease H1; TIM, triosephosphate isomerase; bTRX, bacterial thioredoxin; hTRX, human thioredoxin.

INTRODUCTION The nature of enzymatic rate enhancement entails knowledge of the chemistry of the individual catalytic groups commonly found in enzymes as well as the ensemble of native protein or RNA structures that form a given substrate’s binding site. The chemistry of the different enzymatic catalytic groups can be classifie into four categories: nucleophiles, electrophiles, general-base catalysts,...
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