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G A Petsko

Publications and source records attributed to G A Petsko.

At least 91 records · Page 5Linked to original sources
PubMed1994

X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis.

The X-ray crystallographic structures of the metal-activated enzyme xylose isomerase from Streptomyces olivochromogenes with the substrates D-glucose, 3-O-methyl-D-glucose and in the absence of substrate were determined to 1.96-, 2.19-, and 1.81-A resolution and refined to R-factors of 16.6%, 15.9%, and 16.1%, respectively. Xylose isomerase catalyzes the interconversion between glucose and fructose (xylose and xylulose under physiological conditions) by utilizing two metal cofactors to promote a hydride shift; the metals are bridged by a glutamate residue. This puts xylose isomerase in the small but rapidly growing family of enzymes with a bridged bimetallic active site, in which both metals are involved in the chemical transformation. The substrate 3-O-methylglucose was chosen in order to position the glucose molecule in the observed electron density unambiguously. Of the two essential magnesium ions per active site, Mg-2 was observed to occupy two alternate positions, separated by 1.8 A, in the substrate-soaked structures. The deduced movement was not observed in the structure without substrate present and is attributed to a step following substrate binding but prior to isomerization. The substrates glucose and 3-O-methylglucose are observed in their linear extended forms and make identical interactions with the enzyme by forming ligands to Mg-1 through O2 and O4 and by forming hydrogen bonds with His53 through O5 and Lys182 through O1. Mg-2 has a water ligand that is interpreted in the crystal structure in the absence of substrate as a hydroxide ion and in the presence of substrate as a water molecule. This hydroxide ion may act as a base to deprotonate the glucose O2 and subsequently protonate the product fructose O1 concomitant with hydride transfer. Calculations of the solvent-accessible surface of possible dimers, with and without the alpha-helical C-terminal domain, suggest that the tetramer is the active form of this xylose isomerase.

3-O-Methylglucose↗
PubMed1994

Crystal structure of the K12M/G15A triosephosphate isomerase double mutant and electrostatic analysis of the active site.

The crystal structure of the yeast triosephosphate isomerase (TIM) double mutant K12M/G15A has been solved to 2 A by X-ray diffraction, and the effects of changing the positively charged lysine to the neutral methionine have been analyzed. The mutant enzyme was crystallized in the presence of the tight-binding inhibitor phosphoglycolohydroxamate, under standard conditions for obtaining crystals of the enzyme-inhibitor complex. The crystals obtained were of the same crystal form as the unliganded wild-type enzyme. The three-dimensional structure confirms that the Lys-12 to Met mutation prevents the enzyme from binding substrate and reveals that the reason is electrostatic and not steric. The substrate-binding loop is in its open position and the Met side chain points away from the active site. Overall, the mutant structure is very similar to that of the wild-type unliganded enzyme. The electrostatic potential at the active site of the mutant enzyme is, however, very different from that of the wild type. It has been postulated previously that Lys-12 may play a role in stabilizing the negative charge in the transition state. This K12M/G15A structure suggests that the active-site Lys, which is strictly conserved, is required for TIM to be able to bind its dianionic substrate.

Amino Acid Sequence↗
PubMed1994

Crystal structure of the mutant yeast triosephosphate isomerase in which the catalytic base glutamic acid 165 is changed to aspartic acid.

The three-dimensional structure of the E165D mutant of the glycolytic enzyme yeast triosephosphate isomerase has been determined by X-ray diffraction at a nominal resolution of 2 A. For crystallization, the mutant enzyme was complexed with the tight-binding intermediate analog, phosphoglycolohydroxamate. Comparison with the structure of the wild-type enzyme reveals that, as originally intended, replacement of the catalytic base Glu-165 with the shorter side chain of aspartic acid has increased the distance between the base and the intermediate analog by 1 A. In addition, the catalytic base is oriented in the E165D structure so as to use the anti orbital of the carboxylate for proton abstraction; in the structure of the wild-type enzyme, the syn orbital is oriented for this purpose. It has been hypothesized that the 1000-fold loss in catalytic activity for this mutant triosephosphate isomerase is due either to the use of the less basic anti orbital for proton transfer or to the greater distance between the base and the substrate. The structure of yeast E165D triosephosphate isomerase suggests that both distance and orientation factors contribute to the loss of activity in the mutant enzyme and, therefore, that both factors contribute to the catalytic efficiency of the wild-type enzyme.

Amino Acid Sequence↗
PubMed1994

Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8-A resolution.

The crystal structure of recombinant chicken triosephosphate isomerase (TIM, E.C. 5.3.1.1) complexed with the intermediate analogue phosphoglycolohydroxamate (PGH) has been solved by the method of molecular replacement and refined to an R-factor of 18.5% at 1.8-A resolution. The structure is essentially identical to that of the yeast TIM-PGH complex [Davenport, R. C., et al. (1991) Biochemistry 30, 5821-5826] determined earlier and refined at comparable resolution. This identity extends to the high-energy conformations of the active-site residues Lys13 and Ser211, as well as the positions of several bound water molecules that are retained in the active site when PGH is bound. Comparison with the structure of uncomplexed chicken TIM shows that the catalytic base, Glu165, moves several angstroms when PGH binds. This movement may provide a trigger for a larger conformational change, one of 7 A, in a loop near the active site, which folds down like a lid to shield the bound inhibitor and catalytic residues from contact with bulk solvent. These same conformational changes were seen in crystalline yeast TIM upon binding of PGH; their occurrence here in a different crystal form of TIM eliminates the possibility that they are an artifact of crystal packing.

Amino Acid Sequence↗
PubMed1994

An anion binding site in human aldose reductase: mechanistic implications for the binding of citrate, cacodylate, and glucose 6-phosphate.

Aldose reductase is a NADPH-dependent aldo-keto reductase involved in the pathogenesis of some diabetic and galactosemic complications. The published crystal structure of human aldose reductase [Wilson et al. (1992) Science 257, 81-84] contains a hitherto unexplained electron density positioned within the active site pocket facing the nicotinamide ring of the NADPH and other key active site residues (Tyr48, His110, and Cys298). In this paper we identify the electron density as citrate, which is present in the crystallization buffer (pH 5.0), and provide confirmatory evidence by both kinetic and crystallographic experiments. Citrate is an uncompetitive inhibitor in the forward reaction with respect to aldehyde (reduction of aldehyde), while it is a competitive inhibitor with respect to alcohol in the backward reaction (oxidation of alcohol), indicating that it interacts with the enzyme-NADP(+)-product complex. Citrate can be replaced in the crystalline enzyme complex by cacodylate or glucose 6-phosphate; the structure of each of these complexes shows the specific molecule bound in the active site. All of the structures have been determined to a nominal resolution of 1.76 A and refined to R-factors below 18%. While cacodylate can be bound within the active site under the crystallization conditions, it does not inhibit the wild-type enzyme in solution. Glucose 6-phosphate, however, is a substrate for aldose reductase. The similar location of the negative charges of citrate, cacodylate, and glucose 6-phosphate within the active site suggests an anion-binding site delineated by the C4N of nicotinamide, the OH of Tyr48, and the N epsilon of His110. The location of citrate binding in the active site leads to a plausible catalytic mechanism for aldose reductase.

Aldehyde Reductase↗
PubMed1994

Tyrosine-48 is the proton donor and histidine-110 directs substrate stereochemical selectivity in the reduction reaction of human aldose reductase: enzyme kinetics and crystal structure of the Y48H mutant enzyme.

The active site of human aldose reductase contains two residues, His110 and Tyr48, either of which could be the proton donor during catalysis. Tyr48 is a candidate since its hydroxyl group is in proximity to Lys77 and thus may have an abnormally low pKa value. To distinguish between these possibilities, we used site-directed mutagenesis to create the H110Q and H110A, the Y48F, Y48H, and Y48S, and the K77M mutant enzymes. The two His110 mutants resulted in a 1000-20,000-fold drop in kcat/Km, respectively, for the reduction of DL-glyceraldehyde at pH 7. The Y48F mutation caused total loss of activity, whereas the Y48H and Y48S mutants retained catalytic activity with kcat/Km reduced by 5 orders of magnitude. The K77M mutant is an inactive enzyme. Kinetic studies using xylose stereoisomers show that the wild-type enzyme distinguishes between D-xylose, L-xylose, and D-lyxose up to 150-fold better than the H110A or H110Q mutants. The His110 mutants do not effectively discriminate between these isomers (4-11-fold). The crystal structure of the Y48H mutant refined at 1.8-A resolution shows that the overall structure is not significantly different from the wild-type structure. Electron densities for the histidine side chain and a new water molecule fill the space occupied by Tyr48 in the wild-type enzyme. The water molecule is in hydrogen-bonding distance to the N zeta group of Lys77 and to the N epsilon of His48 and fills the space occupied by the hydroxyl group of tyrosine in the wild-type structure. These findings suggest that proton transfer is mediated in the Y48H mutant enzyme by the water molecule. The Y48H mutant shows large and equal primary deuterium isotope effects on kcat and kcat/Km (1.81 +/- 0.03), providing direct evidence for hydride transfer as the rate-determining step in this mutant. Deuterium solvent isotope effects indicate that the relative contribution of proton transfer to this step of the catalytic cascade is much less important for the Y48H mutant than for the wild-type enzyme [D2O(kcat/Km) = 1.06 +/- 0.02 and 4.73 +/- 0.23, respectively]. The kinetic and mutagenesis data, together with structural data, indicate that His 110 plays an important role in the orientation of substrates in the active site pocket, while Tyr48 is the proton donor during aldehyde reduction by aldose reductase.

Aldehyde Reductase↗
PubMed1994

Isotopic exchange plus substrate and inhibition kinetics of D-xylose isomerase do not support a proton-transfer mechanism.

The D-xylose isomerase of Streptomyces olivochromogenes is a Mg2+- or Mn(2+)-dependent enzyme that catalyzes the aldose-ketose isomerization of xylose to xylulose or of glucose to fructose. Proton exchange into water during enzyme-catalyzed isomerization of C-2 tritiated glucose at 15, 25 and 55 degrees C shows < 0.6% exchange (the loss of one proton in every billion turnovers). High concentrations of guanidine hydrochloride and extremes of pH had no effect on the amount of exchange detected. Such a low percentage of exchange is inconsistent with a proton-transfer mechanism as the main kinetic pathway for isomerization. 19F NMR experiments showed no release of fluoride after incubation of the enzyme for 4 weeks with 800 mM 3-deoxy-3-fluoroglucose or 3-deoxy-3-fluoroallose (both are competitive inhibitors with Ki values of 600 mM). This result is also inconsistent with a proton-transfer mechanism. A hydride-shift mechanism following ring opening has been proposed for the isomerization. Enzyme-catalyzed ring opening was directly measured by demonstrating H2S release upon reaction of xylose isomerase with 1-thioglucose. D-Xylose isomerase-catalyzed interconversion of glucose to fructose exhibited linear Arrhenius behavior with an activation energy of 14 kcal/mol from 0 to 50 degrees C. No change in rate-determining step occurs over this temperature range. 13C NMR experiments with glucose show that enzyme-bound magnesium or manganese does not interact specifically with any one site on the sugar. These results are consistent with nonproductive binding modes for the substrate glucose in addition to productive binding.

Aldose-Ketose Isomerases↗
PubMed1994

Role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase: replacement of a catalytic metal by an amino acid.

The distinct roles of the two magnesium ions essential to the activity of D-xylose isomerase from Streptomyces olivochromogenes were examined. The enzyme-magnesium complex was isolated, and the stoichiometry of cation binding determined by neutron activation analysis to be 2 mol of magnesium per mole of enzyme. A plot of Mg2+ added versus Mg2+ bound to enzyme is consistent with apparent KD values of < or = 0.5-1.0 mM for one Mg2+ and < or = 2-5 mM for the second. A site-directed mutant of D-xylose isomerase was designed to remove the tighter, tetracoordinated magnesium binding site (site 1, Mg-1); Glu180 was replaced with Lys180. The stoichiometry of metal binding to this mutant, E180K, is 1 mol of magnesium per mole of enzyme. Ring-opening assays with 1-thioglucose (H2S released upon ring opening) show E180K catalyzes the opening of the sugar ring at 20% the rate of the wild-type, but E180K does not catalyze isomerization of glucose to fructose. Thus, the magnesium bound to Glu180 is essential for isomerization but not essential for ring opening. The X-ray crystallographic structures of E180K in the absence of magnesium and in the presence and absence of 250 mM glucose were obtained to 1.8-A resolution and refined to R factors of 17.7% and 19.7%, respectively. The wild-type and both E180K structures show no significant structural differences, except the epsilon-amino group of Lys180, which occupies the position usually occupied by the Mg-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Aldose-Ketose Isomerases↗
PubMed1994

The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate.

The mechanism of irreversible inactivation of mandelate racemase (MR) from Pseudomonas putida by alpha-phenylglycidate (alpha PGA) has been investigated stereochemically and crystallographically. The (R) and (S) enantiomers of alpha PGA were synthesized in high enantiomeric excess (81% ee and 83% ee, respectively) using Sharpless epoxidation chemistry. (R)-alpha PGA was determined to be a stereospecific and stoichiometric irreversible inactivator of MR. (S)-alpha PGA does not inactivate MR and appears to bind noncovalently to the active site of MR with less affinity than that of (R)-alpha PGA. The X-ray crystal structure (2.0-A resolution) of MR inactivated by (R)-alpha PGA revealed the presence of a covalent adduct formed by nucleophilic attack of the epsilon-amino group of Lys 166 on the distal carbon on the epoxide ring of (R)-alpha PGA. The proximity of the alpha-proton of (S)-mandelate to Lys 166 [configurationally equivalent to (R)-alpha PGA] was corroborated by the crystal structure (2.1-A resolution) of MR complexed with the substrate analog/competitive inhibitor, (S)-atrolactate [(S)-alpha-methylmandelate]. These results support the proposal that Lys 166 is the polyvalent acid/base responsible for proton transfers on the (S) face of mandelate. In addition, the high-resolution structures also provide insight into the probable interactions of mandelate with the essential Mg2+ and functional groups in the active site.

Alkylation↗
PubMed1994

Analogous inhibitors of elastase do not always bind analogously.

It has been assumed that the structure of a single inhibitor complex is sufficient to define the available subsites of an enzyme that has a unique binding site and a uniquely defined mode for ligand binding--the specificity for these subsites can thus be probed by kinetic experiments. Elastase is an enzyme for which these traditional assumptions, which underlie such structural and kinetic studies, do not hold. Three new crystal structures of elastase complexed to chemically similar inhibitors with similar binding affinities reveal a diversity of binding modes as well as two new subsites on elastase. The existence of multiple binding sites and different binding modes for such similar inhibitors indicates that researchers must proceed with caution when using kinetics to map out protein subsites.

Anilides↗
PubMed1994

Cloning, sequencing, and expression in Escherichia coli of the gene encoding a 45-kilodalton protein, elongation factor Tu, from Chlamydia trachomatis serovar F.

The gene encoding a 45-kDa protein (45K) of Chlamydia trachomatis serovar F was cloned, sequenced, and overexpressed in Escherichia coli. Alignment of the deduced peptide sequence with E. coli elongation factor Tu (EF-Tu) demonstrated 69% identity. The 45K was recognized by a Chlamydia genus-specific monoclonal antibody GP-45 and cross-reacted with a monospecific polyclonal antibody to E. coli EF-Tu. Purified recombinant 45K has the capability to bind GDP, and the binding was enhanced in the presence of E. coli elongation factor Ts (EF-Ts). The GDP binding was specifically inhibited by the monoclonal antibody GP-45. These data suggest that the 45K is a chlamydial EF-Tu, and it forms a functional complex with E. coli EF-Ts protein.

Amino Acid Sequence↗
PubMed1993

Structure of the Mg(2+)-bound form of CheY and mechanism of phosphoryl transfer in bacterial chemotaxis.

The response regulator protein of bacterial chemotaxis, CheY, is representative of a large family of signal transduction proteins that function as phosphorylation-activated switches to regulate the activities of associated effector domains. These regulators catalyze the metal ion-dependent phosphoryl transfer and dephosphorylation reactions that control the effector activities. The crystal structures of Salmonella typhimurium CheY with and without Mg2+ bound at the active site have been determined and refined at 1.8-A resolution. While the overall structures of metal-bound and metal-free CheY are similar, significant rearrangements occur within the active site involving the three most highly conserved residues of the response regulator family. Conservation of the cluster of carboxylate side chains at the active site of response regulator domains can be rationalized in terms of their role in coordinating the catalytically essential divalent metal ion. The Mg2+ coordination geometry provides insights to the mechanism of phosphoryl transfer.

Bacterial Proteins↗
PubMed1993

A novel structural basis for membrane association of a protein: construction of a chimeric soluble mutant of (S)-mandelate dehydrogenase from Pseudomonas putida.

The (S)-mandelate dehydrogenase (MDH) from Pseudomonas putida (ATCC 12633) is the only membrane-associated member of a homologous family of FMN-dependent, alpha-hydroxy acid dehydrogenases/oxidases that includes the structurally characterized glycolate oxidase from spinach (GOX). We have correlated the membrane association of MDH to a polypeptide segment in the interior of the primary sequence. This has been accomplished by construction of a chimeric enzyme in which the putative membrane-binding segment in MDH has been deleted and replaced with the corresponding segment from the soluble GOX. The resulting chimera, MDH-GOX, is soluble and retains partial catalytic activity (approximately 1%) using (S)-mandelate as substrate. In contrast, the activities of both the membrane-associated wild-type MDH and the soluble MDH-GOX are nearly the same when (S)-phenyllactate is used as substrate. To the best of our knowledge, this is the first example of a membrane-associated protein in which an internal polypeptide segment anchors the protein to the membrane.

Alcohol Oxidoreductases↗
PubMed1993

26-10 Fab-digoxin complex: affinity and specificity due to surface complementarity.

We have determined the three-dimensional structures of the antigen-binding fragment of the anti-digoxin monoclonal antibody 26-10 in the uncomplexed state at 2.7 A resolution and as a complex with digoxin at 2.5 A resolution. Neither the antibody nor digoxin undergoes any significant conformational changes upon forming the complex. Digoxin interacts primarily with the antibody heavy chain and is oriented such that the carbohydrate groups are exposed to solvent and the lactone ring is buried in a deep pocket at the bottom of the combining site. Despite extensive interactions between antibody and antigen, no hydrogen bonds or salt links are formed between 26-10 and digoxin. Thus the 26-10-digoxin complex is unique among the known three-dimensional structures of antibody-antigen complexes in that specificity and high affinity arise primarily from shape complementarity.

Amino Acid Sequence↗
PubMed1993

On the origin of enzymatic species.

The diversity of enzyme catalytic function is remarkable, particularly when one considers that ancestral life forms must have started with a much smaller ensemble of proteins. In this article, we discuss the evolution of the mandelate pathway in pseudomonads as an example of how catalytic diversity may have evolved. We suggest that existing enzymes that catalyse the chemistry needed to accomplish a transformation were recruited, followed by the evolution of specific binding.

Binding Sites↗
PubMed1992

Crystallization and preliminary crystallographic analysis of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli.

Aspartate-beta-semialdehyde dehydrogenase catalyzes the NADPH-mediated reductive dephosphorylation of beta-aspartylphosphate at a branch point in the biosynthesis of several amino acids. The enzyme from Escherichia coli has been crystallized by the vapor diffusion method from Tris buffer (pH 8.5) using polyethylene glycol 4000 as a precipitant. The crystals are orthorhombic and have the symmetry of space group P222(1), with unit cell dimensions of a = 177.8 A, b = 59.9 A, c = 118.65 A, and alpha = beta = gamma = 90 degrees. The dimensions and space group are indicative of two enzyme dimers (40 kDa per subunit) in the asymmetric unit. The crystals show strong diffraction, and a native data set has been collected to 2.5 A resolution.

Aspartate-Semialdehyde Dehydrogenase↗