Mechanism of adenylate kinase. Are the essential lysines essential?

Using site-specific mutagenesis, we have probed the structural and functional roles of lysine-21 and lysine-27 of adenylate kinase (AK) from chicken muscle expressed in Escherichia coli. The two residues were chosen since according to the nuclear magnetic resonance (NMR) model [Mildvan, A. S., & Fry, D. C. (1987) Adv. Enzymol. 58, 241-313], they are located near the alpha- and the gamma-phosphates, respectively, of adenosine 5'-triphosphate (ATP) in the AK-MgATP complex. In addition, a lysine residue (Lys-21 in the case of AK) along with a glycine-rich loop is considered "essential" in the catalysis of kinases and other nucleotide binding proteins. The Lys-27 to methionine (K27M) mutant showed only slight increases in kcat and Km, but a substantial increase (1.8 kcal/mol) in the free energy of unfolding, relative to the WT AK. For proper interpretation of the steady-state kinetic data, viscosity-dependent kinetics was used to show that the chemical step is partially rate-limiting in the catalysis of AK. Computer modeling suggested that the folded form of K27M could gain stability (relative to the wild type) via hydrophobic interactions of Met-27 with Val-179 and Phe-183 and/or formation of a charge-transfer complex between Met-27 and Phe-183. The latter was supported by an upfield shift of the methyl protons of Met-27 in 1H NMR. Other than this, the 1H NMR spectrum of K27M is very similar to that of WT, suggesting little perturbation in the global or even local conformations.(ABSTRACT TRUNCATED AT 250 WORDS)

Mechanism of adenylate kinase. Is there a relationship between local substrate dynamics, local binding energy, and the catalytic mechanism?

Adenylyl (beta,gamma-methylene)diphosphonic acid (AMPPCP) labeled with deuterium at the adenine ring ([8-2H]AMPPCP) and at the beta,gamma-methylene group (AMPPCD2P), as well as adenosine 5'-monophosphate labeled at the adenine ring ([8-2H]AMP), was synthesized and used for deuterium nuclear magnetic resonance (NMR) determination of effective correlation times (tau c) of the free nucleotide and the complexes with adenylate kinase (AK). Extensive and rigorous control experiments and theoretical analysis were performed to justify the validity of the experimental approaches, particularly the fast exchange condition, and the reliability of the tau c values obtained. For the free nucleotide, the results suggest that the phosphonate group of free AMPPCP possesses appreciable local mobility relative to the adenine ring and that complexation with Mg2+ greatly reduced such a local mobility. For the complexes with AK, effective tau c values of 7, 15, 28, 28, and 27 ns were obtained for AMPPCD2P, MgAMPPCD2P, [8-2H]AMPPCP, Mg[8-2H]AMPPCP, and [8-2H]AMP, respectively. These results suggest that the adenine ring of substrates is rigidly bound in all cases, that the phosphonate chain of AMPPCP possesses considerable local mobility, and that Mg2+ reduces such local mobility but does not totally immobilize it. The local dynamics of the analogues bound to AK was correlated with local binding energies for the binding of MgAMPPCP and MgATP to AK estimated from the binding studies by proton NMR and other techniques, in conjunction with the binding theory of Jencks [Jencks, W. P. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 4046-4050]. The results suggest that no general correlation exists between the local rigidity of portions of a bound substrate and the corresponding (ground state) local binding energy contributed by these portions. In particular, the adenosine moiety contributes little to the binding energy despite the fact that the adenine ring is rigidly bound; the triphosphate (PPPi) moiety behaves oppositely; Mg2+ immobilizes the triphosphate chain but does not enhance binding. Finally, isomers of the substitution-inert beta,gamma-bidentate Cr(III) complexes of adenosine 5'-triphosphate (CrATP) were used to probe two unresolved catalytic problems implicitly related to the local mobility of the phosphonate chain of AMPPCP in the AK-MgAMPPCP complex. The first problem concerns the result of electron paramagnetic resonance (EPR) studies that (Rp)- but not (Sp)-[beta-17O]ATP caused a line broadening in the Mn(II) EPR spectrum of the AK-MnATP complex [Kalbitzer, H. R., Marquetant, R., Connolly, B. A., & Goody, R. S. (1983) Eur. J. Biochem. 133, 221-227].(ABSTRACT TRUNCATED AT 400 WORDS)

Mechanism of adenylate kinase. Histidine-36 is not directly involved in catalysis, but protects cysteine-25 and stabilizes the tertiary structure.

Several previous reports on muscle adenylate kinase (AK) have suggested that histidine-36 (His-36) is located in the binding site of adenosine 5'-triphosphate (ATP) and is involved in catalysis. We have tested the role of His-36 using site-specific mutagenesis on chicken muscle AK expressed in Escherichia coli. Three mutant proteins (H36Q, H36N, and H36G) were obtained by substituting His-36 with glutamine, asparagine, and glycine, respectively. Steady-state kinetic studies showed that the mutants have similar kinetic properties to those of the wild-type (WT) AK, which suggested that His-36 is not directly involved in catalysis. However, His-36 is likely to interact with or protect cysteine-25 (Cys-25) on the basis of the following evidence: The crystal structure of porcine muscle AK revealed a close proximity between His-36 and Cys-25; the mutants were unstable during purification (the order of stability was WT greater than H36Q greater than H36N greater than H36G); the H36G mutant readily dimerized; the sulfhydryl groups of mutants became more reactive (WT less than H36Q less than H36N) toward 5,5'-dithiobis(2-nitrobenzoic acid). Furthermore, His-36 was found to stabilize the tertiary structure of AK on the basis of guanidine hydrochloride induced denaturation studies, which showed that the conformational stability decreases in the order WT greater than H36Q greater than H36N.(ABSTRACT TRUNCATED AT 250 WORDS)

Further theoretical refinement on the internal thermodynamics of perfect enzymes.

By solving simultaneously the equation for 'uniform binding' [Albery & Knowles (1976) Biochemistry 15, 5631-5640] and the equation for 'differential binding' [Chin (1983) J. Am. Chem. Soc. 105, 6502-6503], I derived the following simple equation for perfect enzymes (with single substrate and single product) under irreversible conditions: K2 = beta(1 + Rs)/1-beta(1 + Rs) where K2 is the internal equilibrium constant and beta is the Brönsted coefficient of the elementary catalytic step, and Rs is defined as [S]0/Ks, with [S]0 being the physiological substrate concentration and Ks being the substrate dissociation constant. The equation suggests that the perfect enzyme can have different internal thermodynamic properties depending on physiological conditions.