SummaryIn 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 pK a of the group and the microenvironment created around the group by the protein or RNA structure, which perturbs its intrinsic pK a to its functional or apparent pK a . These pK a 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 electro- 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 trifluoroketones; hmCK, human muscle creatine kinase; DsbA and DsbC, disulfide 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 disulfide 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.

Three arginine residues (Arg-11, Arg-39, Arg-61) are found at the active site of 4-oxalocrotonate tautomerase in the X-ray structure of the affinity-labeled enzyme [Taylor, A. B., Czerwinski, R. M., Johnson, R. M., Jr., Whitman, C. P., and Hackert, M. L. (1998) Biochemistry 37, 14692-14700]. The catalytic roles of these arginines were examined by mutagenesis, kinetic, and heteronuclear NMR studies. With a 1,6-dicarboxylate substrate (2-hydroxymuconate), the R61A mutation showed no kinetic effects, while the R11A mutation decreased k(cat) 88-fold and increased K(m) 8.6-fold, suggesting both binding and catalytic roles for Arg-11. With a 1-monocarboxylate substrate (2-hydroxy-2,4-pentadienoate), no kinetic effects of the R11A mutation were found, indicating that Arg-11 interacts with the 6-carboxylate of the substrate. The stereoselectivity of the R11A-catalyzed protonation at C-5 of the dicarboxylate substrate decreased, while the stereoselectivity of protonation at C-3 of the monocarboxylate substrate increased in comparison with wild-type 4-OT, indicating the importance of Arg-11 in properly orienting the dicarboxylate substrate by interacting with the charged 6-carboxylate group. With 2-hydroxymuconate, the R39A and R39Q mutations decreased k(cat) by 125- and 389-fold and increased K(m) by 1.5- and 2.6-fold, respectively, suggesting a largely catalytic role for Arg-39. The activity of the R11A/R39A double mutant was at least 10(4)-fold lower than that of the wild-type enzyme, indicating approximate additivity of the effects of the two arginine mutants on k(cat). For both R11A and R39Q, 2D (1)H-(15)N HSQC and 3D (1)H-(15)N NOESY-HSQC spectra showed chemical shift changes mainly near the mutated residues, indicating otherwise intact protein structures. The changes in the R39Q mutant were mainly in the beta-hairpin from residues 50 to 57 which covers the active site. HSQC titration of R11A with the substrate analogue cis, cis-muconate yielded a K(d) of 22 mM, 37-fold greater than the K(d) found with wild-type 4-OT (0.6 mM). With the R39Q mutant, cis, cis-muconate showed negative cooperativity in active site binding with two K(d) values, 3.5 and 29 mM. This observation together with the low K(m) of 2-hydroxymuconate (0.47 mM) suggests that only the tight binding sites function catalytically in the R39Q mutant. The (15)Nepsilon resonances of all six Arg residues of 4-OT were assigned, and the assignments of Arg-11, -39, and -61 were confirmed by mutagenesis. The binding of cis,cis-muconate to wild-type 4-OT upshifts Arg-11 Nepsilon (by 0.05 ppm) and downshifts Arg-39 Nepsilon (by 1.19 ppm), indicating differing electronic delocalizations in the guanidinium groups. A mechanism is proposed in which Arg-11 interacts with the 6-carboxylate of the substrate to facilitate both substrate binding and catalysis and Arg-39 interacts with the 1-carboxylate and the 2-keto group of the substrate to promote carbonyl polarization and catalysis, while Pro-1 transfers protons from C-3 to C-5. This mechanism, together with the effect...

We have compared hydrogen bond lengths on enzymes derived with high precision (I ؎0 .

The catalytic general base, Pro-1, of the enzyme 4-oxalocrotonate tautomerase has been mutated to Gly, Ala, Val, and Leu, residues with aliphatic side chains. The Val mutant was partially (55%) processed by removal of the amino-terminal methionine to yield P1V/M1P2V, while the Leu mutant was not processed and completely retained methionine (M1P2L). The M1P2L mutant lost 2300-fold in kcat with no change in Km, and the residual activity of the unresolvable P1V/M1P2V mixture could be explained by the summation of two activities, one equal to that of M1P2L and the other equal to that of the P1G mutant. The P1G and P1A mutants showed 76- and 58-fold decreases in kcat and much smaller decreases in Km of 4- and 2.8-fold, respectively. The dissociation constant of the substrate analog cis,cis-muconate decreased 1.7-fold in the P1G mutant as determined by NMR titration. 2D 1H-15N HSQC spectra and 3D 1H-15N NOESY HSQC spectra of the 15N-labeled P1G mutant showed no structural differences from the wild-type enzyme except for small changes in backbone 15N and NH chemical shifts at the active site. Both the P1G and P1A mutants showed no change in overall conformation by circular dichroic spectroscopy. Both mutants and the wild-type enzyme generate the S-enantiomer of the product [5-2H]-2-oxo-3-hexenedioate with comparable stereoselectivities indicating a largely intact active site. The P1G and P1A mutants showed 10- and 4-fold decreases, respectively, in catalysis of exchange of the C3 proton of the substrate 2-oxo-1,6-hexanedioate, consistent with the lower basicities of Gly-1 and Ala-1 compared to Pro-1. The pH dependences of kcat/Km for the P1G and P1A mutants revealed pKa values of the general base of 5.3 and 5.9, respectively. NMR titration of the uniformly 15N-labeled P1G mutant showed the pKa of Gly-1 to be < or = 5.6, in agreement with the kinetic data. As with the wild-type enzyme, the active site environments on the P1G and P1A mutants lower the pKa of the general base by at least 2.5 units. It is concluded that the 2 order of magnitude decreases in kcat in the P1G and P1A mutants result from both a decrease in basicity and an increase in flexibility of the general base. The greater 10(3.4)-fold decrease in kcat found with the presence of an additional residue at the amino-terminus is ascribed to either the complete blockage or the drastically altered position of the general base.