Thermal and photochemical epimerization/equilibration of carbohydrate cobaloximes.

Epimeric carbohydrate alkyl cobaloximes 4:5, 9:10, and 12:13 can be equilibrated thermally or photochemically. In each case, one isomer is strongly favored: exo-3-deoxy-3-pyridyldimethylglyoximatocobalt-1,2:5,6-di-O-isopropylidene-alpha-D-glucofuranose 4 for the 4:5 epimer pair, exo-3-deoxy-3-pyridyldimethylglyoximatocobalt-5-O-carboxymethyl-1,2-O-isopropylidene-alpha-D-xylofuranose 9 for the 9:10 epimer pair, and equatorial 1-deoxy-1-pyridyldimethylglyoximatocobalt-2,3,4,6-tetra-O-benzyl-beta-D-glucopyranose 12 for the 12:13 epimer pair. These data indicate that there is a strong facial preference for the coupling of py(dmgH)(2)Co(*) radicals with alkyl R(*) free radicals, with the preferred kinetic path leading to the more stable product.

Probing the radical mechanism of galactose oxidase using an ultrafast radical probe.

Processing of trans-2-phenylcyclopropylmethanols 5 and 6 by the monocopper/tyrosine radical enzyme galactose oxidase led to mechanism-based inactivation with a partition ratio, (k(cat) + k(inact))/k(inact), of approximately 1 and a primary deuterium isotope effect, k(inact(H))/k(inact(D)), of 3.2. The data are consistent with a radical mechanism for galactose oxidase with a short lived ketyl radical anion intermediate.

Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion.

Escherichia coli glycerol kinase (GK) displays "half-of-the-sites" reactivity toward ATP and allosteric regulation by fructose 1, 6-bisphosphate (FBP), which has been shown to promote dimer-tetramer assembly and to inhibit only tetramers. To probe the role of tetramer assembly, a mutation (Ser58-->Trp) was designed to sterically block formation of the dimer-dimer interface near the FBP binding site [Ormo, M., Bystrom, C., and Remington, S. J. (1998) Biochemistry 37, 16565-16572]. The substitution did not substantially change the Michaelis constants or alter allosteric regulation of GK by a second effector, the phosphocarrier protein IIAGlc; however, it eliminated FBP inhibition. Crystal structures of GK in complex with different nontransferable ATP analogues and glycerol revealed an asymmetric dimer with one subunit adopting an open conformation and the other adopting the closed conformation found in previously determined structures. The conformational difference is produced by a approximately 6.0 degrees rigid-body rotation of the N-terminal domain with respect to the C-terminal domain, similar to that observed for hexokinase and actin, members of the same ATPase superfamily. Two of the ATP analogues bound in nonproductive conformations in both subunits. However, beta, gamma-difluoromethyleneadenosine 5'-triphosphate (AMP-PCF2P), a potent inhibitor of GK, bound nonproductively in the closed subunit and in a putative productive conformation in the open subunit, with the gamma-phosphate placed for in-line transfer to glycerol. This asymmetry is consistent with "half-of-the-sites" reactivity and suggests that the inhibition of GK by FBP is due to restriction of domain motion.

Construction and analysis of a semi-quantitative energy profile for the reaction catalyzed by the radical enzyme galactose oxidase.

Galactose oxidase (GOase) is a mononuclear type 2 copper enzyme which oxidizes primary alcohols to aldehydes using molecular oxygen (RCH2OH + O2 = RCHO + H2O2). An unusual crosslink between tyrosine 272 and cysteine 228 provides a modified tyrosine radical site which acts as a ligand for the active site copper and is believed to act as a one-electron redox center. The single active site copper is believed to act as a second one-electron redox center. The use of the tyrosine one-electron redox center and the copper one-electron redox center allows removal of two electrons from alcohol substrate for subsequent transfer to molecular oxygen. Previously, we and others have proposed a detailed step-by-step radical mechanism for the reaction catalyzed by galactose oxidase. The catalytic cycle can be divided into two half reactions. The first half reaction entails transfer of two electrons and two protons from the alcohol substrate to the enzyme to form aldehyde product and two-electron-reduced enzyme (one electron at the tyrosine center and one at the copper center). The second half reaction entails transfer of two electrons and two protons from the two-electron-reduced enzyme to O2 to form H2O2 product and regenerate fully oxidized catalytically active enzyme ready for another catalytic cycle. In this paper, we describe the construction of a semi-quantitative energy profile for this radical mechanism. Several significant points emerge from this analysis. One point is the prediction that galactose oxidase should have an unusually low redox potential for copper, to our knowledge lower than any other redox active copper protein. Another point is that the distorted or entatic copper site causes the unusually low redox potential. A final point is that crosslinking of tyrosine 272 and cysteine 228 alters the redox properties of the tyrosine center to enhance catalysis compared to what would be expected for a normal tyrosine.

Thiols as mechanistic probes for catalysis by the free radical enzyme galactose oxidase.

Galactose oxidase, a mononuclear copper enzyme, oxidizes primary alcohols to aldehydes using molecular oxygen. A unique type of cross-link between tyrosine 272, an active-site copper ligand, and cysteine 228 provides a modified tyrosine radical site believed to act as a one-electron redox center. Substrate analogs incorporating a primary thiol group in place of the primary alcohol group in normal substrates (RCH2OH) have been studied as active-site mechanistic probes. Thiol sulfur coordinates to the active-site copper, leading to enzyme inactivation in a time- and concentration-dependent manner. The mechanism of inactivation involves redox chemistry related to the active-site redox centers, though inactivation does not proceed through the rate-determining hydrogen atom abstraction step that occurs in alcohol oxidation. Thiols are therefore classified as active-site-directed redox inactivators. The thiol analog of galactose, 6-Thio-Me-Gal, is also turned over by the enzyme, albeit at a much reduced rate, indicating that the energetics of turnover is changed significantly. Thiols constitute a particularly good model of the ground state enzyme-substrate complex. The Michaelis complex for thiol substrate analogs is stabilized at least 200-fold compared to the analogous alcohol substrates, whereas the transition state of H atom abstraction is destabilized, presumably due to a slight increase in distances of reacting atoms and weakening of hydrogen-bonding interactions due to the larger atomic radius of sulfur compared to that of oxygen.

Structure of the complex of L-benzylsuccinate with wheat serine carboxypeptidase II at 2.0-A resolution.

The structure of the complex of L-benzylsuccinate (Ki = 0.2 mM) bound to wheat serine carboxypeptidase II has been analyzed at 2.0-A resolution for native and inhibited crystals at -170 degrees C. The model has been refined and has a standard crystallographic R-factor of 0.176 for 57,734 reflections observed between 20.0- and 2.0-A resolution. The root mean square deviation from ideal bonds is 0.017 A and from ideal angles is 2.6 degrees. The model consists of 400 amino acids, 4 N-linked saccharide residues, and 430 water molecules. L-Benzylsuccinate occupies a narrow slot in the active site defined by Tyr 60, Tyr 239, and the polypeptide backbone. One carboxylate forms hydrogen bonds to Glu 145, Asn 51, the amide of Gly 52, and the catalytic His 397, suggestive of how the peptide C-terminal carboxylate is recognized by the enzyme. The phenyl ring stacks between Tyr 239 and Tyr 60, while the other carboxylate occupies the "oxyanion hole". One of the oxygens accepts hydrogen bonds from the amides of Tyr 147 and Gly 53, while the other forms a very close contact (2.3 A) with the O gamma of Ser 146, forcing the side chain into a conformation alternative to that found in the resting state of the enzyme. The inhibitor occupies the active site in a way that suggests that it can be regarded as a transition-state analogue of serine carboxypeptidases. The model suggests a novel enzymatic mechanism, involving substrate-assisted catalysis, that might account for the low pH optimum (4.0-5.5) of peptidase activity unique to this family of serine proteinases.

Proposed mechanism for the condensation reaction of citrate synthase: 1.9-A structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme A.

The crystal structure of the ternary complex citrate synthase-oxaloacetate-carboxymethyl coenzyme A has been solved to a resolution of 1.9 A and refined to a conventional crystallographic R factor of 0.185. The structure resembles a proposed transition state of the condensation reaction and suggests that the condensation reaction proceeds through a neutral enol rather than an enolate intermediate. A mechanism for the condensation reaction is proposed which involves the participation of three key catalytic groups (Asp 375, His 274, and His 320) in two distinct steps. The proposed mechanism invokes concerted general acid-base catalysis twice to explain both the energetics of the reaction and the experimentally observed inversion of stereochemistry at the attacking carbon atom.

Conformations and electronic structures of oxidized and reduced isoalloxazine.

The conformations of oxidized and reduced isoalloxazine have been examined by a molecular orbital method, PRDDO (partial retention of diatomic differential overlap). The angle theta of fold about the N...N line of the central ring is zero for the planar oxidized form, but a bend of theta = 10 degrees requires only 2 kcal/mol. On the other hand, the reduced form is nonplanar (theta approximately 15 degrees), and the barrier for reversal of this bend is 4 kcal/mol, comparable with that in simple amines. Molecular properties and reactivity are interpreted in terms of charge and orbital distributions, and localized molecular orbitals have been derived by the method of Boys.