PubMed HealthSearch

Biomedical subjects

W N Lipscomb

Publications and source records attributed to W N Lipscomb.

At least 19 recordsLinked to original sources

Separation of inhibition and activation of the allosteric yeast chorismate mutase.

Yeast chorismate mutase (EC 5.4.99.5) shows homotropic activation by the substrate, allosteric activation by tryptophan, and allosteric inhibition by tyrosine. In this study mutants of chorismate mutase have been found that remain sensitive to one allosteric effector (tryptophan) but insensitive to the other (tyrosine). These mutations are located in the catalytic domain: loop 220s (212-226) and helix 12 (227-251). The first example starts with the Thr-266 --> Ile mutant that had previously been shown to be locked in the activated R state. The additional mutation Ile-225 --> Thr unlocks the R state and restores the activation by tryptophan but not the inhibition by tyrosine. The second example refers to a molecular trigger for the switch between the T and R state: a hydrogen-bonded system, which stabilizes only the T state, from Tyr-234 to Glu-23 to Arg-157. Various mutants of Tyr-234, especially Tyr-234 --> Phe, are unresponsive to tyrosine but are activated by tryptophan. This separation of activation from inhibition may indicate a pathway for activation that is independent of the allosteric transition and may also be consistent with an intermediate structure between T and R states.

Allosteric Regulation

Mechanisms of catalysis and allosteric regulation of yeast chorismate mutase from crystal structures.

BACKGROUND: Chorismate mutase (CM) catalyzes the Claisen rearrangement of chorismate to prephenate, notably the only known enzymatically catalyzed pericyclic reaction in primary metabolism. Structures of the enzyme in complex with an endo-oxabicyclic transition state analogue inhibitor, previously determined for Bacillus subtilis and Escherichia coli CM, provide structural insight into the enzyme mechanism. In contrast to these bacterial CMs, yeast CM is allosterically regulated in two ways: activation by tryptophan and inhibition by tyrosine. Yeast CM exists in two allosteric states, R (active) and t (inactive). RESULTS: We have determined crystal structures of wild-type yeast CM cocrystallized with tryptophan and an endo-oxabicyclic transition state analogue inhibitor, of wild-type yeast CM co-crystallized with tyrosine and the endo-oxabicyclic transition state analogue inhibitor and of the Thr226-->Ser mutant of yeast CM in complex with tryptophan. Binding of the transition state analogue inhibitor to CM keeps the enzyme in a 'super R' state, even if the inhibitory effector tyrosine is bound to the regulatory site. CONCLUSIONS: The endo-oxabicyclic inhibitor binds to yeast CM in a similar way as it does to the distantly related CM from E. coli. The inhibitor-binding mode supports a mechanism by which polar sidechains of the enzyme bind the substrate in the pseudo-diaxial conformation, which is required for catalytic turnover. A lysine and a protonated glutamate sidechain have a critical role in the stabilization of the transition state of the pericyclic reaction. The allosteric transition from T-->R state is accompanied by a 15 degrees rotation of one of the two subunits relative to the other (where 0 degrees rotation defines the T state). This rotation causes conformational changes at the dimer interface which are transmitted to the active site. An allosteric pathway is proposed to include residues Phe28, Asp24 and Glu23, which move toward the activesite cavity in the T state. In the presence of the transition-state analogue a super R state is formed, which is characterised by a 22 degrees rotation of one subunit relative to the other.

Bacillus subtilis

The crystal structure of human interferon beta at 2.2-A resolution.

Type I interferons (IFNs) are helical cytokines that have diverse biological activities despite the fact that they appear to interact with the same receptor system. To achieve a better understanding of the structural basis for the different activities of alpha and beta IFNs, we have determined the crystal structure of glycosylated human IFN-beta at 2.2-A resolution by molecular replacement. The molecule adopts a fold similar to that of the previously determined structures of murine IFN-beta and human IFN-alpha2b but displays several distinct structural features. Like human IFN-alpha2b, human IFN-beta contains a zinc-binding site at the interface of the two molecules in the asymmetric unit, raising the question of functional relevance for IFN-beta dimers. However, unlike the human IFN-alpha2b dimer, in which homologous surfaces form the interface, human IFN-beta dimerizes with contact surfaces from opposite sides of the molecule. The relevance of the structure to the effects of point mutations in IFN-beta at specific exposed residues is discussed. A potential role of ligand-ligand interactions in the conformational assembly of IFN receptor components is discussed.

Computer Simulation

A glutamate residue in the catalytic center of the yeast chorismate mutase restricts enzyme activity to acidic conditions.

Chorismate mutase acts at the first branchpoint of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. Comparison of the x-ray structures of allosteric chorismate mutase from the yeast Saccharomyces cerevisiae with Escherichia coli chorismate mutase/prephenate dehydratase suggested conserved active sites between both enzymes. We have replaced all critical amino acid residues, Arg-16, Arg-157, Lys-168, Glu-198, Thr-242, and Glu-246, of yeast chorismate mutase by aliphatic amino acid residues. The resulting enzymes exhibit the necessity of these residues for catalytic function and provide evidence of their localization at the active site. Unlike some bacterial enzymes, yeast chorismate mutase has highest activity at acidic pH values. Replacement of Glu-246 in the yeast chorismate mutase by glutamine changes the pH optimum for activity of the enzyme from a narrow to a broad pH range. These data suggest that Glu-246 in the catalytic center must be protonated for maximum catalysis and restricts optimal activity of the enzyme to low pH.

Chorismate Mutase

Crystal structure of the T state of allosteric yeast chorismate mutase and comparison with the R state.

The crystal structure of the tyrosine-bound T state of allosteric yeast Saccharomyces cerevisiae chorismate mutase was solved by molecular replacement at a resolution of 2.8 angstroms using a monomer of the R-state structure as the search model. The allosteric inhibitor tyrosine was found to bind in the T state at the same binding site as the allosteric activator tryptophan binds in the R state, thus defining one regulatory binding site for each monomer. Activation by tryptophan is caused by the larger steric size of its side chain, thereby pushing apart the allosteric domain of one monomer and helix H8 of the catalytic domain of the other monomer. Inhibition is caused by polar contacts of tyrosine with Arg-75 and Arg-76 of one monomer and with Gly-141, Ser-142, and Thr-145 of the other monomer, thereby bringing the allosteric and catalytic domains closer together. The allosteric transition includes an 8 degree rotation of each of the two catalytic domains relative to the allosteric domains of each monomer (domain closure). Alternatively, this transition can be described as a 15 degree rotation of the catalytic domains of the dimer relative to each other.

Allosteric Site

Kinetics and mechanisms of activation and inhibition of porcine liver fructose-1,6-bisphosphatase by monovalent cations.

K+ and Li+ were used to study the kinetic effects of monovalent cations on porcine liver fructose-1,6-bisphosphatase (FBPase). At saturating fructose 1,6-bisphosphate (FBP) concentrations, Li+ was found to be a linear noncompetitive inhibitor with respect to Mg2+. K+ was found to activate the wild-type enzyme at low concentrations (K(m) = 17 mM) and to inhibit the enzyme at high concentrations (K(IK+) = 68mM). A steady-state random ter mechanism was proposed, and a mathematical equation was derived to account for the Mg2+ and K+ kinetics and activation of FBPase. Interestingly, when Glu280 was mutated to glutamine by site-directed mutagenesis, K+ lost the ability to activate the enzyme and became a noncompetitive inhibitor with respect to Mg2+. These kinetic data suggest that K+ has two distinct sites. One is a high-affinity activation site and the other a low-affinity inhibition site. Glu280 is essential for allowing K+ to bind at the activation site. Due to the geometric constraints and its small atomic radius, Li+ can bind only at the inhibitory site. It is postulated that monovalent cations activate FBPase by helping the Arg276 residue "deshield" the partial negative charge on the 1-phosphoryl group of the substrate so that nucleophilic attack on the 1-phosphorus atom is facilitated. In addition, the monovalent cations may, along with Mg2+ ions and surrounding residues of the protein, help orient the 1-phosphoryl group so as to achieve the optimal position required for catalysis. Monovalent cations inhibit FBPase either by distorting the geometry of the active site or by retarding turnover or product release.

Animals

Two-metal ion mechanism of bovine lens leucine aminopeptidase: active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography.

The three-dimensional structures of bovine lens leucine aminopeptidase (blLAP) complexed with L-leucinal and of the unliganded enzyme have been determined at crystallographic resolutions of 1.9 and 1.6 A, respectively. Leucinal binds as a hydrated gem-diol to the active site of b1LAP), resembling the presumed gem-diolated intermediate in the catalytic pathway. One hydroxyl group bridges the two active site metal ions, and the other OH group is coordinated to Zn1. The high-resolution structure of the unliganded enzyme reveals one metal-bound water ligand, which is bridging both zinc ions. Together, these structures support a mechanism in which the bridging water ligand is the attacking hydroxide ion nucleophile. The gem-diolate intermediate is probably stabilized by four coordinating bonds to the dizinc center and by interaction with Lys-262 and Arg-336. In the mechanism, Lys-262 polarizes the peptide carbonyl group, which is also coordinated to Zn1. The Arg-336 side chain interacts with the substrate and the gem-diolate intermediate via water molecules. Near Arg-336 in the b1LAP-leucinal structure, an unusually short hydrogen bond is found between two active site water molecules.

Animals

Location of the active site of allosteric chorismate mutase from Saccharomyces cerevisiae, and comments on the catalytic and regulatory mechanisms.

The active site of the allosteric chorismate mutase (chorismate pyruvatemutase, EC 5.4.99.5) from yeast Saccharomyces cerevisiae (YCM) was located by comparison with the mutase domain (ECM) of chorismate mutase/prephenate dehydratase [prephenate hydro-lyase (decarboxylating), EC 4.2.1.51] (the P protein) from Escherichia coli. Active site domains of these two enzymes show very similar four-helix bundles, each of 94 residues which superimpose with a rms deviation of 1.06 A. Of the seven active site residues, four are conserved: the two arginines, which bind to the inhibitor's two carboxylates; the lysine, which binds to the ether oxygen; and the glutamate, which binds to the inhibitor's hydroxyl group in ECM and presumably in YCM. The other three residues in YCM (ECM) are Thr-242 (Ser-84), Asn-194 (Asp-48), and Glu-246 (Gln-88). This Glu-246, modeled close to the ether oxygen of chorismate in YCM, may function as a polarizing or ionizable group, which provides another facet to the catalytic mechanism.

Allosteric Regulation

Crystallographic evidence for the action of potassium, thallium, and lithium ions on fructose-1,6-bisphosphatase.

Fructose-1,6-bisphosphatase (Fru-1,6-Pase; D-fructose-1,6-bisphosphate 1-phosphohydrolase, EC 3.1.3.11) requires two divalent metal ions to hydrolyze alpha-D-fructose 1,6-bisphosphate. Although not required for catalysis, monovalent cations modify the enzyme activity; K+ and Tl+ ions are activators, whereas Li+ ions are inhibitors. Their mechanisms of action are still unknown. We report here crystallographic structures of pig kidney Fru-1,6-Pase complexed with K+, Tl+, or both Tl+ and Li+. In the T form Fru-1,6-Pase complexed with the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate (AhG-1,6-P2) and Tl+ or K+ ions, three Tl+ or K+ binding sites are found. Site 1 is defined by Glu-97, Asp-118, Asp-121, Glu-280, and a 1-phosphate oxygen of AhG-1,6-P2; site 2 is defined by Glu-97, Glu-98, Asp-118, and Leu-120. Finally, site 3 is defined by Arg-276, Glu-280, and the 1-phosphate group of AhG-1,6-P2. The Tl+ or K+ ions at sites 1 and 2 are very close to the positions previously identified for the divalent metal ions. Site 3 is specific to K+ or Tl+. In the divalent metal ion complexes, site 3 is occupied by the guanidinium group of Arg-276. These observations suggest that Tl+ or K+ ions can substitute for Arg-276 in the active site and polarize the 1-phosphate group, thus facilitating nucleophilic attack on the phosphorus center. In the T form complexed with both Tl+ and Li+ ions, Li+ replaces Tl+ at metal site 1. Inhibition by lithium very likely occurs as it binds to this site, thus retarding turnover or phosphate release. The present study provides a structural basis for a similar mechanism of inhibition for inositol monophosphatase, one of the potential targets of lithium ions in the treatment of manic depression.

Allosteric Regulation

Transition state analogue L-leucinephosphonic acid bound to bovine lens leucine aminopeptidase: X-ray structure at 1.65 A resolution in a new crystal form.

The three-dimensional structure of bovine lens leucine aminopeptidase (blLAP) complexed with L-Leucinephosphonic acid (LeuP) has been determined by molecular replacement using the structure of native blLAP as a starting model. Cocrystallization of the enzyme with the inhibitor yielded a new crystal form of space group P321 which has cell dimensions a = 130.4 A and c = 125.4 A. Refinement of the model against data from 7.0 to 1.65 A resolution resulted in a final structure with a crystallographic residual of 0.160 (R(free) = 0.191). The N-terminal amino group of LeuP is coordinated to Zn-489, one phosphoryl oxygen atom bridges both metal ions, and another phosphoryl oxygen atom is coordinated to Zn-488. The side chain of Arg-336 interacts with the inhibitor via three water molecules. LeuP resembles the presumed tetrahedral gem-diolate transition state after direct attack of a water or hydroxide ion nucleophile on the scissile peptide bond. On the basis of the LeuP binding mode and the previous structural and biochemical data, three plausible reaction pathways are evaluated. The two-metal ion mechanisms discussed herein share as common features a metal-bound hydroxide ion nucleophile and polarization of the carbonyl group by the zinc ions. Possible catalytic roles of Arg-336 and Lys-262 in the direct or indirect (through H2O) protonation of the leaving group, in the stabilization of a zinc-bound OH- nucleophile and in the stabilization of the negatively charged intermediate, are discussed. A site 3 metal ion approximately 12 A away from the active site 2 zinc ion probably serves a structural role.

Amino Acid Sequence

The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.

Many organisms expand the information content of their genome through enzymatic methylation of cytosine residues. Here we report the 2.8 A crystal structure of a bacterial DNA (cytosine-5)-methyltransferase (DCMtase), M. HaeIII, bound covalently to DNA. In this complex, the substrate cytosine is extruded from the DNA helix and inserted into the active site of the enzyme, as has been observed for another DCMtase, M. HhaI. The DNA is bound in a cleft between the two domains of the protein and is distorted from the characteristic B-form conformation at its recognition sequence. A comparison of structures shows a variation in the mode of DNA recognition: M. HaeIII differs from M. HhaI in that the remaining bases in its recognition sequence undergo an extensive rearrangement in their pairing. In this process, the bases are unstacked, and a gap 8 A long opens in the DNA.

Amino Acid Sequence

Crystal structure of spinach chloroplast fructose-1,6-bisphosphatase at 2.8 A resolution.

The three-dimensional structure of the spinach chloroplast fructose-1,6-bisphosphatase (Fru-1,6-Pase) has been solved by the molecular replacement method at 2.8 A resolution and refined to a crystallographic R factor of 0.203. The enzyme is composed of four monomers and displays pseudo D2 symmetry. Comparison with the allosteric Fru-1,6-Pase from pig kidney shows orientationally displaced dimers within the quaternary structure of the chloroplast enzyme. When the C1C2 dimers of the two enzymes are superimposed, the C3C4 dimer of the chloroplast enzyme is rotated 20 degrees and 5 degrees relative to the C3C4 dimer of the R and T forms of the pig kidney enzyme, respectively. This new quaternary structure, designated as S, may be described as a super-T form and is outside of the pathway of the allosteric transition which occurs in the pig kidney enzyme, which shows a 15 degrees rotation between T and R forms. Chloroplast Fru-1,6-Pase, unlike the pig kidney enzyme, is insensitive to allosteric transformation by AMP. Structural changes in the AMP binding site involving mainly helices H1, H2, and H3 and the loop between H1 and H2 at the dimer interface interfere with binding of the phosphate of AMP. Finally, the location of cysteines residues provides a basis for a preliminary discussion of the activation of the enzyme by reduction of cysteines via the ferredoxin-thioredoxin f system; this process is complementary to activation by pH changes, Mg2+ or Ca2+, Fru-1,6-P2, and possibly Fru-2,6-P2.

Adenosine Monophosphate

Structural aspects of the allosteric inhibition of fructose-1,6-bisphosphatase by AMP: the binding of both the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate and catalytic metal ions monitored by X-ray crystallography.

The crystal structures of the T form pig kidney fructose-1,6-bisphosphatase (EC 3.1.3.11) complexed with AMP, the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate (AhG-1,6-P2), and Mn2+ at concentrations of 5, 15, 100, and 300 microM have been determined and refined at resolutions of 2.1-2.3 A to R factors which range from 0.180 to 0.195, respectively. Two metal ions per active site have been identified, one at a binding site of high affinity (metal site 1'), the second in a low affinity site (metal site 2'). The 1-phosphate group of the substrate analogue coordinates to the metal ion at site 1', but not at site 2'. In these four complexes, the distances between the two metal ions are all within 0.2 A of 4.3 A. In the previously determined R form structure of Fru-1,6-Pase complexed with AhG-1,6-P2 and Mn2+, there are also two metal ions in the active site at metal sites 1 and 2. The metal ion at site 1 is only 0.6 A displaced from the metal ion at site 1' in the T form and is also coordinated to the 1-phosphate group of AhG-1,6-P2. However, the second metal ion is located in two distinct sites which are 1.4 A apart in the T and R form structures. In the R form the Mn2+ at site 2 is coordinated to the 1-phosphate group of the substrate analogue. This metal ion is apparently required to orient the phosphate group for nucleophilic attack at the phosphorus center.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenosine Monophosphate

Crystal structure of fructose-1,6-bisphosphatase complexed with fructose 2,6-bisphosphate, AMP, and Zn2+ at 2.0-A resolution: aspects of synergism between inhibitors.

The crystal structure of fructose-1,6-bisphosphatase (Fru-1,6-Pase; EC 3.1.3.11) complexed with Zn2+ and two allosteric regulators, AMP and fructose 2,6-bisphosphate (Fru-2,6-P2) has been determined at 2.0-A resolution. In the refined model, the crystallographic R factor is 0.189 with rms deviations of 0.014 A and 2.8 degrees from ideal geometries for bond lengths and bond angles, respectively. A 15 degrees rotation is observed between the upper dimer C1C2 and the lower dimer C3C4 relative to the R-form structure (fructose 6-phosphate complex), consistent with that expected from a T-form structure. The major difference between the structure of the previously determined Fru-2,6-P2 complex (R form) and that of the current quaternary T-form complex lies in the active site domain. A zinc binding site distinct from the three binding sites established earlier was identified within each monomer. Helix H4 (residues 123-127) was found to be better defined than in previously studied ligated Fru-1,6-Pase structures. Interactions between monomers in the active site domain were found involving H4 residues from one monomer and residues Tyr-258 and Arg-243 from the adjacent monomer. Cooperativity between AMP and Fru-2,6-P2 in signal transmission probably involves the following features: an AMP site, the adjacent B3 strand (residues 113-118), the metal site, the immediate active site, the short helix H4 (residues 123-127), and Tyr-258 and Arg-243 from the adjacent monomer within the upper (or lower) dimer. The closest distance between the immediate active site and that on the adjacent monomer is only 5 A. Thus, the involvement of H4 in signal transmission adds another important pathway to the scheme of the allosteric mechanism of Fru-1,6-Pase.

Adenosine Monophosphate

Toward a mechanism for the allosteric transition of pig kidney fructose-1,6-bisphosphatase.

We examine structural aspects of the allosteric transition of pig kidney fructose-1,6-bisphosphatase (Fru-1,6-Pase) by analyzing the X-ray structures of the R and T form enzymes. The results show a hierarchical structural change during the R to T transition. Upon binding of AMP, a cascade of structural changes occurs starting from the AMP site: expansion of the AMP site, local conformational changes of helices H1 and H2, independent rotations and translation of helices H1, H2 and H3 (and loops connecting them), reorganization of the AMP domain as a whole and its 1.9 degrees rotation relative to the fructose-1,6-bisphosphate domain, and conformational changes at the C1-C2 and C1-C4 interfaces leading to the quaternary conformational change of a 17 degrees rotation between dimers. The AMP inhibition results from the relative movement between the AMP and FBP domains which distorts the active site during the transition by shifting the metal binding sites to unfavourable positions. Communication that ensures cooperativity during R to T transition relies on changes in positions of helices H1, H2 and H3, loops 127-131, 168-170 and 187-192, and on N-terminal residues. All of these features are close to the C1-C4 and symmetry equivalent C2-C3 interfaces and the relatively small C1-C3 interface of the T form. These secondary structures form the framework along which structural changes due to AMP binding can propagate to other parts of the monomers as well as across monomer interfaces. Future dynamics studies may be useful to analyze initiation, propagation and completion of the quaternary conformational change of Fru-1,6-Pase upon AMP binding. Also, site directed mutagenesis experiments are expected to provide more detailed descriptions of the importance of each of the residues that has been identified here in the proposed mechanisms.

Adenosine Monophosphate

The crystal structure of allosteric chorismate mutase at 2.2-A resolution.

The crystal structure of an allosteric chorismate mutase, the Thr-226-->Ile mutant, from yeast Saccharomyces cerevisiae has been determined to 2.2-A resolution by using the multiple isomorphous replacement method. Solvent-flattening and electron-density modification were applied for phase improvement. The current crystallographic R factor is 0.196. The final model includes 504 of the 512 residues and 97 water molecules. In addition, two tryptophan molecules were identified in the interface between monomers. The overall structure is completely different from the reported structure of chorismate mutase from Bacillus subtilis. This structure showed 71% helices with essentially no beta-sheet structures.

Allosteric Regulation

The crystallization and preliminary X-ray analysis of allosteric chorismate mutase.

An allosteric chorismate mutase, the Thr226-->Ile mutant, from the yeast Saccharomyces cerevisiae has been crystallized in space group P6(1)(P6(5)) using the hanging drop vapour diffusion method at room temperature. The cell dimensions are a = b = 95.8 A, c = 157.9 A, alpha = beta = 90 degrees, gamma = 120 degrees. It contains a dimer in the crystallographic asymmetric unit. The crystal diffracts to 2.2 A resolution. A native data set has been collected to 82% completeness at this resolution.

Allosteric Regulation

The monofunctional chorismate mutase from Bacillus subtilis. Structure determination of chorismate mutase and its complexes with a transition state analog and prephenate, and implications for the mechanism of the enzymatic reaction.

Structures have been determined for chorismate mutase from Bacillus subtilis and of complexes of this enzyme with product and an endo-oxabicyclic transition state analog using multiple isomorphous replacement plus partial structure phase combination and non-crystallographic averaging. In addition to 522 water molecules, the model includes 1380 of the 1524 amino acid residues of the four trimers (each containing 3 x 127 amino acid residues) in the asymmetric unit. Refinement to 1.9 A resolution yields 0.194 for R and r.m.s. deviations from ideal values of 0.014 A for bond lengths and 2.92 degrees for bond angles. The trimer resembles a beta-barrel structure in which a core beta-sheet is surrounded by helices. The structures of the two complexes locate the active sites which are at the interfaces of adjacent pairs of monomers in the trimer. These structures have been refined at 2.2 A to a crystallographic R value of 0.18 and show r.m.s. deviations from ideal values of 0.013 A for bond lengths and 2.84 degrees or 3.05 degrees for bond angles, respectively. The final models have 1398 amino acid residues, nine prephenate molecules and 503 water molecules in the product complex, and 1403 amino acid residues, 12 inhibitor molecules and 530 water molecules in the transition state complex. The active sites of all three of these structures are very similar and provide a structural basis for the biochemical studies that indicate a pericyclic mechanism for conversion of chorismate to prephenate. The absence of reactive catalytic residues on the enzyme, the selective binding of the single reactive conformation of chorismate, the stabilization of the polar transition state, and the possible role of the C-terminal region in "capping" the active site are factors which relate these structures to the million-fold rate enhancement of this reaction.

Amino Acid Sequence