Michele Cianci

The molecular basis of the coloration mechanism in lobster shell: β-Crustacyanin at 3.2-Å resolution

The binding of the carotenoid astaxanthin (AXT) in the protein multimacromolecular complex crustacyanin (CR) is responsible for the blue coloration of lobster shell. The structural basis of the bathochromic shift mechanism has long been elusive. A change in color occurs from the orange red of the unbound dilute AXT (λmax 472 nm in hexane), the well-known color of cooked lobster, to slate blue in the protein-bound live lobster state (λmax 632 nm in CR). Intriguingly, extracted CR becomes red on dehydration and on rehydration goes back to blue. Recently, the innovative use of softer x-rays and xenon derivatization yielded the three-dimensional structure of the A1 apoprotein subunit of CR, confirming it as a member of the lipocalin superfamily. That work provided the molecular replacement search model for a crystal form of the β-CR holo complex, that is an A1 with A3 subunit assembly including two bound AXT molecules. We have thereby determined the structure of the A3 molecule de novo. Lobster has clearly evolved an intricate structural mechanism for the coloration of its shell using AXT and a bathochromic shift. Blue/purple AXT proteins are ubiquitous among invertebrate marine animals, particularly the Crustacea. The three-dimensional structure of β-CR has identified the protein contacts and structural alterations needed for the AXT color regulation mechanism.

X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy

X-ray absorption spectroscopy is exquisitely sensitive to the coordination geometry of an absorbing atom and therefore allows bond distances and angles of the surrounding atomic cluster to be measured with atomic resolution. By contrast, the accuracy and resolution of metalloprotein active sites obtainable from x-ray crystallography are often insufficient to analyze the electronic properties of the metals that are essential for their biological functions. Here, we demonstrate that the combination of both methods on the same metalloprotein single crystal yields a structural model of the protein with exceptional active-site resolution. To this end, we have collected an x-ray diffraction data set to 1.4-Å resolution and Fe K-edge polarized x-ray absorption near edge structure (XANES) spectra on the same cyanomet sperm whale myoglobin crystal. The XANES spectra were quantitatively analyzed by using a method based on the multiple scattering approach, which yielded Fe-heme structural parameters with ±(0.02–0.07)-Å accuracy on the atomic distances and ±7° on the Fe–CN angle. These XANES-derived parameters were subsequently used as restraints in the crystal structure refinement. By combining XANES and x-ray diffraction, we have obtained an cyanomet sperm whale myoglobin structural model with a higher precision of the bond lengths and angles at the active site than would have been possible with crystallographic analysis alone.

The interdependence of wavelength, redundancy and dose in sulfur SAD experiments.

In the last decade, the popularity of sulfur SAD anomalous dispersion experiments has spread rapidly among synchrotron users as a quick and streamlined way of solving the phase problem in macromolecular crystallography. On beamline 10 at SRS (Daresbury Laboratory, UK), a versatile design has allowed test data sets to be collected at six wavelengths between 0.979 and 2.290 A in order to evaluate the importance and the interdependence of experimental variables such as the Bijvoet ratio, wavelength, resolution limit, data redundancy and absorbed X-ray dose in the sample per data set. All the samples used in the experiments were high-quality hen egg-white lysozyme crystals. X-radiation damage was found to affect disulfide bridges after the crystals had been given a total dose of 0.20 x 10(7) Gy. However, with such a total dose, it was still possible in all cases to find a strategy to collect data sets to determine the sulfur substructure and produce good-quality phases by choosing an optimum combination of wavelength, exposure time and redundancy. A |Delta(ano)|/sigma(Delta(ano)) greater than 1.5 for all resolution shells was a necessary requirement for successful sulfur SAD substructure location. Provided this is achieved, it seems possible to find an optimum compromise between wavelength, redundancy and dose to provide phasing information. The choice of the wavelength should then follow the sample composition and the diffracting properties of the crystal. For strongly diffracting crystals, wavelengths equal or shorter than 1.540 A can be selected to capture the available data (provided the Bijvoet ratio is reasonable), while a longer wavelength, to gain as high a Bijvoet ratio as possible, must be used for more weakly diffracting crystals. These results suggest that an approach to a sulfur SAD experiment based on a complete description of the crystal system and the instrument for data collection is useful.

Anomalous scattering in structural chemistry and biology

The uses of X-ray anomalous scattering in crystal structure analysis have undergone a major expansion due to the refinement and ease of availability of the necessary X-ray instrumentation and methods. The structural chemistry and biology fields span a similar suite of technical needs but with widely differing molecular systems. The innate synergies between the two research fields brought two of the authors (JRH and VK) together at an Erice Summer School on Synchrotron Radiation in Crystallography in 1985 and took them into a collaboration spanning already 20 years. The authors’ wide perspectives are therefore, if not unique, perhaps rather rare. Thus the breadth of coverage of this review is unusual. However, there are two excellent books on anomalous scattering and its uses that have been published covering the periods up to 1975 and 1994 [S. Ramaseshan, S.C. Abrahams (Eds). Anomalous Scattering, Munksgaard, Copenhagen (1975); G. Materlik, C.J. Sparks, K. Fischer (Eds). Resonant Anomalous X-ray Scattering: Theory and Applications, North Holland, Amsterdam (1994)]. As the number of examples of applications in structural biology are now so many it has only been possible to select some illustrative examples but with surveys of trends. In addition though, the development of the methodologies is described in more detail. The structural chemistry applications in, for example, microporous materials, superconductors and magnetic materials is expanding fast but still at a stage where we could attempt to provide a detailed coverage of results, which we have done. Anomalous scattering results on locating metal atoms can also be compared with other technique results and so sections on X-ray Absorption Spectroscopy (XAS), Diffraction Anomalous Fine Structure (DAFS), neutron diffraction and Nuclear Magnetic Resonance (NMR) applications are described where they relate to metal atom location and local structure. Finally anomalous scattering has also been very useful to help develop the modern synchrotron Laue method for quantitative crystal structure analysis, which is also briefly described. ¶Dedicated to Professor Durward W. J. Cruickshank, FRS, Emeritus Professor of Chemistry, The University of Manchester, on the occasion of his 82nd Birthday, 7 March 2006. Durward is an inspiration to us all as a scientist with many fine contributions spanning nearly 60 years, as well as a friend, mentor and colleague to several of us for many years. Contents  Introduction 246 1. Brief resume of anomalous scattering 252  1.1.Principles 252  1.2.Different nomenclatures in use for the anomalous scattering coefficients 255  1.3.Some crystal symmetry and diffraction data measurement key facts 258  1.4.Absolute structure: the key definitions 260 2. Some historical notes: the absolute configuration of (R, R)-(1)-tartaric acid was determined by J. M. Bijvoet and colleagues (1951) 262 3. The use of anomalous scattering in structural chemistry 264  3.1.Introduction to site-specific, neighbouring element and valence contrast experiments 264  3.2.Overview of neighbouring element and valence contrast experiments 265  3.3.Applications of anomalous scattering to particular classes of materials 277  3.4.Potential applications of anomalous dispersion in powder diffraction structure solution de novo 290  3.5.The determination of the absolute configuration or hand of smaller molecules using crystallography 292 4. The use of anomalous scattering in structural biology 293  4.1.Previous reviews of the uses of anomalous scattering in protein crystallography especially SR 293  4.2.The location of the anomalous scatterers 296  4.3.MIR, SIROAS and MAD phasing 296  4.4.The recent growth of Single-wavelength Anomalous Dispersion(SAD) phasing 299  4.5.Identification of metals in metalloproteins (Mn, Zn, Cu, Ca) and ions (Cl − , ) in proteins including case studies 307  4.6.Instrumentation case study: line 10 at the SRS 309 5. Use of anomalous scattering derived structural details to help develop the Laue method 311 6. Complementary methods 314  6.1.XAS 314  6.2.Diffraction Anomalous Fine Structure Analysis (The DAFS method) 317  6.3.Neighbouring atom contrast by neutron diffraction methods 319  6.4.Magnetic resonance spectroscopy 320 7. Concluding remarks 323 Acknowledgements 324 References 325 Subject index 333

Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation

Lipases (EC 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates, such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of considerable physiological significance with high interest also for their industrial applications. The hydrolysis reaction follows a two-step mechanism, or “interfacial activation,” with adsorption of the enzyme to a heterogeneous interface and subsequent enhancement of the lipolytic activity. Among lipases, Candida antarctica lipase B (CALB) has never shown any significant interfacial activation, and a closed conformation of CALB has never been reported, leading to the conclusion that its behavior was due to the absence of a lid regulating the access to the active site. The lid open and closed conformations and their protonation states are observed in the crystal structure of CALB at 0.91 Å resolution. Having the open and closed states at atomic resolution allows relating protonation to the conformation, indicating the role of Asp145 and Lys290 in the conformation alteration. The findings explain the lack of interfacial activation of CALB and offer new elements to elucidate this mechanism, with the consequent implications for the catalytic properties and classification of lipases.

Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness.

A bond-distance analysis has been undertaken to determine the protonation states of ionizable amino acids in trypsin, subtilisin and lysozyme. The diffraction resolutions were 1.2 Å for trypsin (97% complete, 12% H-atom visibility at 2.5σ), 1.26 Å for subtilisin (100% complete, 11% H-atom visibility at 2.5σ) and 0.65 Å for lysozyme (PDB entry 2vb1; 98% complete, 30% H-atom visibility at 3σ). These studies provide a wide diffraction resolution range for assessment. The bond-length e.s.d.s obtained are as small as 0.008 Å and thus provide an exceptional opportunity for bond-length analyses. The results indicate that useful information can be obtained from diffraction data at around 1.2-1.3 Å resolution and that minor increases in resolution can have significant effects on reducing the associated bond-length standard deviations. The protonation states in histidine residues were also considered; however, owing to the smaller differences between the protonated and deprotonated forms it is much more difficult to infer the protonation states of these residues. Not even the 0.65 Å resolution lysozyme structure provided the necessary accuracy to determine the protonation states of histidine.

The crystal structure of Sporosarcina pasteurii urease in a complex with citrate provides new hints for inhibitor design

Urease, the enzyme that catalyses the hydrolysis of urea, is a virulence factor for a large number of ureolytic bacterial human pathogens. The increasing resistance of these pathogens to common antibiotics as well as the need to control urease activity to improve the yield of soil nitrogen fertilization in agricultural applications has stimulated the development of novel classes of molecules that target urease as enzyme inhibitors. We report on the crystal structure at 1.50-Å resolution of a complex formed between citrate and urease from Sporosarcina pasteurii, a widespread and highly ureolytic soil bacterium. The fit of the ligand to the active site involves stabilizing interactions, such as a carboxylate group that binds the nickel ions at the active site and several hydrogen bonds with the surrounding residues. The citrate ligand has a significantly extended structure compared with previously reported ligands co-crystallized with urease and thus represents a unique and promising scaffold for the design of new, highly active, stable, selective inhibitors.

Fluoride inhibition of Sporosarcina pasteurii urease: structure and thermodynamics

Urease is a nickel-dependent enzyme and a virulence factor for ureolytic bacterial human pathogens, but it is also necessary to convert urea, the most worldwide used fertilizer, into forms of nitrogen that can be taken up by crop plants. A strategy to control the activity of urease for medical and agricultural applications is to use enzyme inhibitors. Fluoride is a known urease inhibitor, but the structural basis of its mode of inhibition is still undetermined. Here, kinetic studies on the fluoride-induced inhibition of urease from Sporosarcina pasteurii, a widespread and highly ureolytic soil bacterium, were performed using isothermal titration calorimetry and revealed a mixed competitive and uncompetitive mechanism. The pH dependence of the inhibition constants, investigated in the 6.5–8.0 range, reveals a predominant uncompetitive mechanism that increases by increasing the pH, and a lesser competitive inhibition that increases by lowering the pH. Ten crystal structures of the enzyme were independently determined using five crystals of the native form and five crystals of the protein crystallized in the presence of fluoride. The analysis of these structures revealed the presence of two fluoride anions coordinated to the Ni(II) ions in the active site, in terminal and bridging positions. The present study consistently supports an interaction of fluoride with the nickel centers in the urease active site in which one fluoride competitively binds to the Ni(II) ion proposed to coordinate urea in the initial step of the catalytic mechanism, while another fluoride uncompetitively substitutes the Ni(II)-bridging hydroxide, blocking its nucleophilic attack on urea.

P13, the EMBL macromolecular crystallography beamline at the low-emittance PETRA III ring for high- and low-energy phasing with variable beam focusing

The P13 macromolecular crystallography beamline, based on the low-emittance source PETRA III, enables X-ray diffraction experiments on macromolecular crystals over a wide wavelength range (0.7–3.1 Å). The beam has a variable focus size and a small divergence enabling data collection on micrometre-sized crystals.

The crystal structure of Erwinia amylovora levansucrase provides a snapshot of the products of sucrose hydrolysis trapped into the active site.

Levansucrases are members of the glycoside hydrolase family and catalyse both the hydrolysis of the substrate sucrose and the transfer of fructosyl units to acceptor molecules. In the presence of sufficient sucrose, this may either lead to the production of fructooligosaccharides or fructose polymers. Aim of this study is to rationalise the differences in the polymerisation properties of bacterial levansucrases and in particular to identify structural features that determine different product spectrum in the levansucrase of the Gram-negative bacterium Erwinia amylovora (Ea Lsc, EC 2.4.1.10) as compared to Gram-positive bacteria such as Bacillus subtilis levansucrase. Ea is an enterobacterial pathogen responsible for the Fire Blight disease in rosaceous plants (e.g., apple and pear) with considerable interest for the agricultural industry. The crystal structure of Ea Lsc was solved at 2.77 Å resolution and compared to those of other fructosyltransferases from Gram-positive and Gram-negative bacteria. We propose the structural features, determining the different reaction products, to reside in just a few loops at the rim of the active site funnel. Moreover we propose that loop 8 may have a role in product length determination in Gluconacetobacter diazotrophicus LsdA and Microbacterium saccharophilum FFase. The Ea Lsc structure shows for the first time the products of sucrose hydrolysis still bound in the active site.