Crystallographic study of turkey egg-white lysozyme and its complex with a disaccharide

The crystal structure of turkey egg-white lysozyme, determined by the molecular replacement method at 5 Å resolution (Bott & Sarma, 1976) has now been refined to 2.8 Å resolution and a model has been built to fit the electron density. A comparison of the co-ordinates with those of hen lysozyme indicate a rootmean-square deviation of 1.6 Å for all the main-chain and side-chain atoms. A significant difference is observed in the region of residues 98 to 115 of the structure. The molecules are packed in this crystal form with the entire length of the active cleft positioned in the vicinity of the crystallographic 6-fold axis and is not blocked by neighboring molecules. A difference electron density map calculated between crystals of turkey lysozyme soaked in a disaccharide of N-acetyl glucosamine—N-acetyl muramic acid and the native crystals showed a strong positive peak at subsite C, a weak positive peak at subsite D and two strong peaks that correspond to the subsite E and a new subsite F′. This new site F′ is different from the subsite F predicted for the sixth saccharide from model building in hen lysozyme. The interactions between the saccharides bound at subsites E and F′ and the enzyme molecules are discussed.     

Crystallization and main-chain structure of neutral protease from Streptomyces caespitosus

A neutral protease, i.e., a zinc-containing metalloendoprotease from Streptomyces caespitosus, has been crystallized using acetone as a precipitating agent. The crystals diffract to better than 1.5 A resolution when a rotating anode X-ray generator is used as an X-ray source. Protein phase angles were calculated by the multiple isomorphous replacement method using two heavy-atom derivatives (HgCl2 and CH3HgCl). A 6 A resolution electron density map clearly showed molecular boundaries. Although its amino acid sequence is not known, the folding pattern of the polypeptide chain could be traced on a 2.5 A resolution electron density map. A large cleft, which is located on the molecular surface, was proved to be the active site of the enzyme by structure analyses of inhibitor-complex crystals. The highest electron density peak, which corresponds to the cleft, was assigned to a catalytically essential zinc atom on difference Fourier synthesis between native and EDTA-soaked crystals.     

Calcium binding sites in tomato bushy stunt virus visualized by Laue crystallography

We have collected Laue diffraction data from crystals of tomato bushy stunt virus using the full white X-ray spectrum from the wiggler magnet of the Synchrotron Radiation Source at Daresbury, U.K. A single 24 second exposure of a crystal soaked in EDTA yielded a data set that was 90% complete between 6 and 3.5 A resolution. A large proportion of the data could be measured using an overlap deconvolution routine to separate spatially overlapping reflections in the dense Laue photograph. Reflections with I greater than 2 sigma I (40% of the data set) were subjected to wavelength normalization. A difference Fourier map between these reflections and a monochromatic native set showed, after icosahedral averaging, the three pairs of Ca2+ binding sites related by quasi-symmetry and the movement of a liganding loop in the protein at the A/C subunit interface. The extent and quality of the data obtained from a single Laue photograph of this virus were thus sufficient to detect clearly such small structural alterations. In a second experiment, a Laue photograph was taken from a crystal that was soaked first in EDTA and then in GdCl3. A difference Fourier map between this Laue data set and the Laue data set from the EDTA-soaked crystal showed clearly the Gd3+ sites in the capsid, demonstrating that the Laue technique is a reliable and efficient means for data collection with virus crystals.     

A structural basis for the interaction of urea with lysozyme.

The effect of urea on the crystal structure of hen egg-white lysozyme has been investigated using X-ray crystallography. High resolution structures have been determined from crystals grown in the presence of 0, 0.7, 2, 3, 4, and 5 M urea and from crystals soaked in 9 M urea. All the forms are essentially isomorphous with the native type II crystals, and the derived structures exhibit excellent geometry and RMS differences from ideality in bond distances and angles. Comparison of the urea complex structures with the native enzyme (type II form, at 1.5 A resolution) indicates that the effect of urea is minimal over the concentration range studied. The mean difference in backbone conformation between the native enzyme and its urea complexes varies from 0.18 to 0.49 A. Conformational changes are limited to flexible surface loops (Thr 69-Asn 74, Ser 100-Asn 103), the active site loop (Asn 59-Cys 80), and the C-terminus (Cys 127-Leu 129). Urea molecules are bound to distinct sites on the surface of the protein. One molecule is bound to the active site cleft's C subsite, at all concentrations, in a fashion analogous to that of the N-acetyl substituent of substrate and inhibitor sugars normally bound to this site. Occupation of this subsite by urea alone does not appear to induce the conformational changes associated with inhibitor binding.     

Structures of deoxy and carbonmonoxy haemoglobin Kansas in the deoxy quaternary conformation.

Haemoglobin Kansas (Asn102(G4)β → Thr) is the only widely studied mutant or modified haemoglobin having four functional haems and displaying lower than normal oxygen affinity. Two forms of this mutant have been investigated by X-ray diffraction. The deoxy form, whose crystals are isomorphous with the native form, has been examined directly by the difference Fourier technique (3.4 Å). In addition to the replaced residue itself, the difference electron density map shows signs of slight movements throughout the region between α and β haem pockets. However, neither type of chain shows stereochemical evidence of a very abnormal oxygen affinity in the tetramer. The nature of the perturbation is different from that proposed in the earlier, low-resolution study of Greer (1971a). Exposure of deoxy crystals to carbon monoxide produces two new crystal forms similar but not identical to the native deoxy form. One of these structures has been solved by rotation and translation function methods and a difference map between carbonmonoxy haemoglobin Kansas in the deoxy quaternary structure and native deoxy haemoglobin has been calculated at 3.5 Å resolution. Carbon monoxide molecules are observed at three of the four haems, and two unidentified large peaks³ appear next to the sulphydryl groups of Cys93β. None of the interchain salt bridges which stabilize the deoxy quaternary state appears to be broken, but large tertiary structural changes are seen in the liganded chains. It seems that when the molecule is subjected to the lattice constraints of the deoxy crystal, the salt bridges do not break upon ligand binding, even though the pH dependence of the first Adair constant and the linearity of proton release with ligand uptake both imply that this does happen to stripped HbA in solution.     

Electron crystallography of bacteriorhodopsin with millisecond time resolution

The goal of time-resolved crystallographic experiments is to capture dynamic "snapshots" of molecules at different stages of a reaction pathway. In recent work, we have developed approaches to determine determined light-induced conformational changes in the proton pump bacteriorhodopsin by electron crystallographic analysis of two-dimensional protein crystals. For this purpose, crystals of bacteriorhodopsin were deposited on an electron microscopic grid and were plunge-frozen in liquid ethane at a variety of times after illumination. Electron diffraction patterns were recorded either from unilluminated crystals or from crystals frozen as early as 1 ms after illumination and used to construct projection difference Fourier maps at 3.5-A resolution to define light-driven changes in protein conformation. As demonstrated here, the data are of a sufficiently high quality that structure factors obtained from a single electron diffraction pattern of a plunge-frozen bacteriorhodopsin crystal are adequate to obtain an interpretable difference Fourier map. These difference maps report on the nature and extent of light-induced conformational changes in the photocycle and have provided incisive tools for understanding the molecular mechanism of proton transport by bacteriorhodopsin.     

Crystallographic analysis of the binding of NADPH, NADPH fragments, and NADPH analogues to glutathione reductase

The binding of the substrate NADPH as well as a number of fragments and derivatives of NADPH to glutathione reductase from human erythrocytes has been investigated by using X-ray crystallography. Crystals of the enzyme were soaked with the compounds of interest, and then the diffraction intensities were collected out to a resolution of 3 A. By use of phase information from the refined structure of the native enzyme in its oxidized state, electron density maps could be calculated. Difference Fourier electron density maps with coefficients Fsoak - Fnative showed that the ligands tested bound either at the functional NADPH binding site or not at all. Electron density maps with coefficients 2Fsoak - Fnative were used to estimate occupancies for various parts of the bound ligands. This revealed that all ligands except NADPH and NADH, which were fully bound, showed differential binding between the adenine end and the nicotinamide end of the molecule: The adenine end always bound with a higher occupancy than the nicotinamide end. Models were built for the protein-ligand complexes and subjected to restrained refinement at 3-A resolution. The mode of binding of NADPH, including the conformational changes of the protein, is described. NADH binding is clearly shown to involve a trapped inorganic phosphate at the position normally occupied by the 2'-phosphate of NADPH. A comparison of the binding of NADPH with the binding of the fragments and analogues provides a structural explanation for their relative binding affinities. In this respect, proper charge and hydrogen-bonding characteristics of buried parts of the ligand seem to be particularly important.     

Three-dimensional structure of bovine pancreatic DNase I at 2.5 A resolution

The three-dimensional structure of bovine pancreatic deoxyribonuclease I (DNase I) has been determined at 2.5 A resolution by X-ray diffraction from single crystals. An atomic model was fitted into the electron density using a graphics display system. DNase I is an alpha, beta-protein with two 6-stranded beta-pleated sheets packed against each other forming the core of a 'sandwich'-type structure. The two predominantly anti-parallel beta-sheets are flanked by three longer alpha-helices and extensive loop regions. The carbohydrate side chain attached to Asn 18 is protruding by approximately 15 A from the otherwise compact molecule of approximate dimensions 45 A X 40 A. The binding site of CA2+-deoxythymidine-3',5'-biphosphate (Ca-pdTp) has been determined by difference Fourier techniques confirming biochemical results that the active centre is close to His 131. Ca-pdTp binds at the surface of the enzyme between the two beta-pleated sheets and seems to interact with several charged amino acid side chains. Active site geometry and folding pattern of DNase I are quite different from staphylococcal nuclease, the only other Ca2+-dependent deoxyribonuclease whose structure is known at high resolution. The electron density map indicates that two Ca2+ ions are bound to the enzyme under crystallization conditions.     

The lactose permease of Escherichia coli: overall structure, the sugar-binding site and the alternating access model for transport

Membrane transport proteins transduce free energy stored in electrochemical ion gradients into a concentration gradient and are a major class of membrane proteins, many of which play important roles in human health and disease. Recently, the X-ray structure of the Escherichia coli lactose permease (LacY), an intensively studied member of a large group of related membrane transport proteins, was solved at 3.5 A. LacY is composed of N- and C-terminal domains, each with six transmembrane helices, symmetrically positioned within the molecule. The structure represents the inward-facing conformation, as evidenced by a large internal hydrophilic cavity open to the cytoplasmic side. The structure with a bound lactose homolog reveals the sugar-binding site in the cavity, and a mechanism for translocation across the membrane is proposed in which the sugar-binding site has alternating accessibility to either side of the membrane.     

Crystallographic study of the complex between sulfite and bakers' yeast flavocytochrome b2

The complex between Saccharomyces cerevisiae flavocytochrome b2 and the sulfite anion has been analyzed by x-ray diffraction. A map of the difference in electron density between the complex and the native protein has been computed. One positive peak of electron density is visible at the active site of each of the two subunits in the asymmetric unit, very close to the N-5 of the flavin. The molecular fragment SO3(2-) can account for the shape of this difference in electron density. A third peak is visible in the subunit containing pyruvate, the reaction product. It is a peak of negative electron density localized at the position where the pyruvate usually is in the native form. These results are interpreted on the basis of the mechanism defined in solution for the reaction between flavins and sulfite.     

Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate

High-resolution nitrite soaked oxidized and reduced crystal structures of two active site mutants, D98N and H255N, of nitrite reductase (NIR) from Alcaligenes faecalis S-6 were determined to better than 2.0 A resolution. In the oxidized D98N nitrite-soaked structures, nitrite is coordinated to the type II copper via its oxygen atoms in an asymmetric bidentate manner; however, elevated B-factors and weak electron density indicate that both nitrite and Asn98 are less ordered than in the native enzyme. This disorder likely results from the inability of the N delta 2 atom of Asn98 to form a hydrogen bond with the bound protonated nitrite, indicating that the hydrogen bond between Asp98 and nitrite in the native NIR structure is essential in anchoring nitrite in the active site for catalysis. In the oxidized nitrite soaked H255N crystal structure, nitrite does not displace the ligand water and is instead coordinated in an alternative mode via a single oxygen to the type II copper. His255 is clearly essential in defining the nitrite binding site despite the lack of direct interaction with the substrate in the native enzyme. The resulting pentacoordinate copper site in the H255N structure also serves as a model for a proposed transient intermediate in the catalytic mechanism consisting of a hydroxyl and nitric oxide molecule coordinated to the copper. The formation of an unusual dinuclear type I copper site in the reduced nitrite soaked D98N and H255N crystal structures may represent an evolutionary link between the mononuclear type I copper centers and dinuclear Cu(A) sites.     

Lead ion binding and RNA chain hydrolysis in phenylalanine tRNA

Crystalline complexes of yeast phenylalanine tRNA and Lead (II) ion were prepared by soaking pregrown orthorhombic crystals of tRNA in saturated lead chloride solutions. The locations of tightly bound lead ions on the tRNA were determined by difference Fourier methods. There are three major lead binding sites; two of these replace tightly bound magnesium ions in the native tRNA structure. Site I is located in the dihydrouridine loop of the molecule adjacent to phosphate P18 which is specifically cleaved by lead. This is evident from changes observed in the Pb-native difference electron density maps. A possible mechanism for lead ion hydrolysis of the polynucleotide chain is proposed.     

Molecular basis of chromium insulin interactions

The physiological role of chromium (III) in diabetes mellitus has been an area of inconclusive research for many years. It is of great interest to explore the interactions made by chromium (III) to get a better insight into their role in glucose metabolism. To understand the molecular basis of chromium action we have carried out spectroscopic and crystallographic investigations on the binding of Cr(III)-Salen with insulin, as Cr(III)-Salen is reported to result in the enhancement of insulin activity. The Cr(III)-insulin complex formation has been characterised at two pHs, viz., 3.5 and 9.0 using UV-Vis and fluorescence studies. The crystallographic analysis of Cr(III)-Salen soaked cubic insulin crystals, using anomalous difference Fourier method, revealed B21 Glu to be the binding site for chromium (III).     

Energetics of galactose- and glucose-aromatic amino acid interactions: implications for binding in galactose-specific proteins

An aromatic amino acid is present in the binding site of a number of sugar binding proteins. The interaction of the saccharide with the aromatic residue is determined by their relative position as well as orientation. The position-orientation of the saccharide relative to the aromatic residue was found to vary in different sugar-binding proteins. In the present study, interaction energies of the complexes of galactose (Gal) and of glucose (Glc) with aromatic residue analogs have been calculated by ab initio density functional (U-B3LYP/ 6-31G**) theory. The position-orientations of the saccharide with respect to the aromatic residue observed in various Gal-, Glc-, and mannose-protein complexes were chosen for the interaction energy calculations. The results of these calculations show that galactose can interact with the aromatic residue with similar interaction energies in a number of position-orientations. The interaction energy of Gal-aromatic residue analog complex in position-orientations observed for the bound saccharide in Glc/Man-protein complexes is comparable to the Glc-aromatic residue analog complex in the same position-orientation. In contrast, there is a large variation in interaction energies of complexes of Glc- and of Gal- with the aromatic residue analog in position-orientations observed in Gal-protein complexes. Furthermore, the conformation wherein the O6 atom is away from the aromatic residue is preferred for the exocyclic -CH2OH group in Gal-aromatic residue analog complexes. The implications of these results for saccharide binding in Gal-specific proteins and the possible role of the aromatic amino acid to ensure proper positioning and orientation of galactose in the binding site have been discussed.     

Lead Ion Binding and RNA Chain Hydrolysis in Phenylalanine tRNA

Abstract

Crystalline complexes of yeast phenylalanine tRNA and Lead (II) ion were prepared by soaking pregrown orthorhombic crystals of tRNA in saturated lead chloride solutions. The locations of tightly bound lead ions on the tRNA were determined by difference Fourier methods. There are three major lead binding sites; two of these replace tightly bound magnesium ions in the native tRNA structure. Site I is located in the dihydrouridine loop of the molecule adjacent to phosphate P18 which is specifically cleaved by lead. This is evident from changes observed in the Pb-native difference electron density maps. A possible mechanism for lead ion hydrolysis of the polynucleotide chain is proposed.     

Carbohydrate binding sites in a pancreatic alpha-amylase-substrate complex, derived from X-ray structure analysis at 2.1 A resolution.

The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC 3.2.1.1.) that was soaked with the substrate maltopentaose showed electron density corresponding to two independent carbohydrate recognition sites on the surface of the molecule. Both binding sites are distinct from the active site described in detail in our previous high-resolution study of a complex between PPA and a carbohydrate inhibitor (Qian M, Buisson G, Duée E, Haser H, Payan F, 1994, Biochemistry 33:6284-6294). One of the binding sites previously identified in a 5-A-resolution electron density map, lies at a distance of 20 A from the active site cleft and can accommodate two glucose units. The second affinity site for sugar units is located close to the calcium binding site. The crystal structure of the maltopentaose complex was refined at 2.1 A resolution, to an R-factor of 17.5%, with an RMS deviation in bond distances of 0.007 A. The model includes all 496 residues of the enzyme, 1 calcium ion, 1 chloride ion, 425 water molecules, and 3 bound sugar rings. The binding sites are characterized and described in detail. The present complex structure provides the evidence of an increased stability of the structure upon interaction with the substrate and allows identification of an N-terminal pyrrolidonecarboxylic acid in PPA.     

5-A Fourier map of gramicidin A phased by deuterium-hydrogen solvent difference neutron diffraction

Crystals of ion-free gramicidin A (P212121: a = 24.61, b = 32.28, c = 32.52) have been investigated using neutron diffraction. A difference analysis of crystals soaked in ethanol/H2O as opposed to ethanol-d6/D2O has led to single isomorphous replacement Fourier projections of the structure at 5-A resolution. The gramicidin dimer appears to be a 32-A-long cylinder oriented parallel to the c-axis in these crystals.     

The coenzyme analogue adenosine 5-diphosphoribose displaces FAD in the active site of p-hydroxybenzoate hydroxylase. An x-ray crystallographic investigation

p-Hydroxybenzoate hydroxylase (PHBH) is an NADPH-dependent enzyme. To locate the NADPH binding site, the enzyme was crystallized under anaerobic conditions in the presence of the substrate p-hydroxybenzoate, the coenzyme analogue adenosine 5-diphosphoribose (ADPR), and sodium dithionite. This yielded colorless crystals that were suitable for X-ray analysis. Diffraction data were collected up to 2.7-A resolution. A difference Fourier between data from these colorless crystals and data from yellow crystals of the enzyme-substrate complex showed that in the colorless crystals the flavin ring was absent. The adenosine 5'-diphosphate moiety, which is the common part between FAD and ADPR, was still present. After restrained least-squares refinement of the enzyme-substrate complex with the riboflavin omitted from the model, additional electron density appeared near the pyrophosphate, which indicated the presence of an ADPR molecule in the FAD binding site of PHBH. The complete ADPR molecule was fitted to the electron density, and subsequent least-squares refinement resulted in a final R factor of 16.8%. Replacement of bound FAD by ADPR was confirmed by equilibrium dialysis, where it was shown that ADPR can effectively remove FAD from the enzyme under mild conditions in 0.1 M potassium phosphate buffer, pH 8.0. The empty pocket left by the flavin ring is filled by solvent, leaving the architecture of the active site and the binding of the substrate largely unaffected.