Ingrid Zegers

Arsenate reductase from S. aureus plasmid pI258 is a phosphatase drafted for redox duty

Arsenate reductase (ArsC) from Staphylococcus aureus plasmid pI258 plays a role in bacterial heavy metal resistance and catalyzes the reduction of arsenate to arsenite. The structures of the oxidized and reduced forms of ArsC were solved. ArsC has the PTPase I fold typical for low molecular weight tyrosine phosphatases (LMW PTPases). Remarkably, kinetic experiments show that pI258 ArsC also catalyzes the tyrosine phosphatase reaction in addition to arsenate reduction. These results provide evidence that ArsC from pI258 evolved from LMW PTPase by the grafting of a redox function onto a pre-existing catalytic site and that its evolutionary origin is different from those of arsenate reductases from Escherichia coli plasmid R773 and from Saccharomyces cerevisiae. The mechanism proposed here for the catalysis of arsenate reduction by pI258 ArsC involves a nucleophilic attack by Cys 10 on arsenate, the formation of a covalent intermediate and the transport of oxidative equivalents by a disulfide cascade. The reaction is associated with major structural changes in the ArsC.

All intermediates of the arsenate reductase mechanism, including an intramolecular dynamic disulfide cascade

The mechanism of pI258 arsenate reductase (ArsC) catalyzed arsenate reduction, involving its P-loop structural motif and three redox active cysteines, has been unraveled. All essential intermediates are visualized with x-ray crystallography, and NMR is used to map dynamic regions in a key disulfide intermediate. Steady-state kinetics of ArsC mutants gives a view of the crucial residues for catalysis. ArsC combines a phosphatase-like nucleophilic displacement reaction with a unique intramolecular disulfide bond cascade. Within this cascade, the formation of a disulfide bond triggers a reversible “conformational switch” that transfers the oxidative equivalents to the surface of the protein, while releasing the reduced substrate.

Crystallization of ornithine acetyltransferase from yeast by counter-diffusion and preliminary X-ray study

A study is presented on the crystallization of ornithine acetyltransferase from yeast, which catalyzes the fifth step in microbial arginine synthesis. The use of the counter-diffusion technique removes the disorder present in one dimension in crystals grown by either the batch or hanging-drop techniques. This makes the difference between useless crystals and crystals that allow successful determination of the structure of the protein. The crystals belong to space group P4, with unit-cell parameters a = b = 66.98, c = 427.09 A, and a data set was collected to 2.76 A.

Cloning, preliminary characterization and crystallization of nucleoside hydrolases from Caenorhabditis elegans and Campylobacter jejuni.

The nucleoside hydrolases (NHs) are a family of nucleoside-modifying enzymes. They play an important role in the purine-salvage pathway of many pathogenic organisms which are unable to synthesize purines de novo. Although well characterized in protozoan parasites, their precise function and mechanism remain unclear in other species. For the first time, NHs from Caenorhabditis elegans and Campylobacter jejuni, which are representatives of mesozoa and bacteria, respectively, have been cloned and purified. Steady-state kinetics indicate a different substrate-specificity profile to previously described hydrolases. Native diffraction data sets were collected from crystals of NH from each organism. The hexagonal crystals (space group P6(2)22 or P6(4)22) of NH from C. elegans diffracted to a resolution of 2.8 A, while the data set from the orthorhombic crystals (space group I222 or I2(1)2(1)2(1)) of NH from C. jejuni could be processed to 1.7 A resolution. The unit-cell parameters were a = b = 102.23, c = 117.27 A in the former case and a = 101.13, b = 100.13, c = 81.37 A in the latter.

Structural Study of the Type II 3-Dehydroquinate Dehydratase from Actinobacillus Pleuropneumoniae

The structure of the type II dehydroquinate dehydratase (DHQase) from Actinobacillus pleuropneumoniae, the third enzyme of the shikimate pathway, has been determined. Crystals diffracting to 1.7 A were obtained in space and on earth using the counter-diffusion technique. The structure was solved using molecular replacement and refined to high resolution. The overall structure of the dodecameric enzyme is described and compared with structures of DHQases from other bacteria. DHQases contain a flexible loop that presumably closes over the active site upon substrate binding. The enzyme can exist in an open or closed conformation. The present structure displays the open conformation, with a sulfate anion bound in the active site. The availability of this structure opens a route to structure-based antibiotics targetting this pathogenic bacterium.

Counterdiffusion protein crystallisation in microgravity and its observation with PromISS (Protein Microscope for the International Space Station)

The crystallisation by counterdiffusion is a very efficient technique for obtaining high-quality protein crystals. A prerequisite for the use of counterdiffusion techniques is that mass transport must be controlled by diffusion alone. Sedimentation and convection can be avoided by either working in gelled systems, working in systems of small dimensions, or in the absence of gravity. We present the results from experiments performed on the ISS using the Protein Microscope for the International Space Station (PromISS), using digital holography to visualise crystal growth processes. We extensively characterised three model proteins for these experiments (cablys3*lysozyme, triose phosphate isomerase, and parvalbumin) and used these to assess the ISS as an environment for crystallisation by counterdiffusion. The possibility to visualise growth and movement of crystals in different types of experiments (capillary counterdiffusion and batch-type) is important, as movement of crystals is clearly not negligible.

Protein crystallization in hydrogel beads

The use of hydrogel beads for the crystallization of proteins is explored in this contribution. The dynamic behaviour of the internal precipitant, protein concentration and relative supersaturation in a gel bead upon submerging the bead in a precipitant solution is characterized theoretically using a transient diffusion model. Agarose and calcium alginate beads have been used for the crystallization of a low-molecular-weight (14.4 kDa, hen egg-white lysozyme) and a high-molecular-weight (636.0 kDa, alcohol oxidase) protein. Entrapment of the protein in the agarose-gel matrix was accomplished using two methods. In the first method, a protein solution is mixed with the agarose sol solution. Gel beads are produced by immersing drops of the protein-agarose sol mixture in a cold paraffin solution. In the second method (which was used to produce calcium alginate and agarose beads), empty gel beads are first produced and subsequently filled with protein by diffusion from a bulk solution into the bead. This latter method has the advantage that a supplementary purification step is introduced (for protein aggregates and large impurities) owing to the diffusion process in the gel matrix. Increasing the precipitant, gel concentration and protein loading resulted in a larger number of crystals of smaller size. Consequently, agarose as well as alginate gels act as nucleation promoters. The supersaturation in a gel bead can be dynamically controlled by changing the precipitant and/or the protein concentration in the bulk solution. Manipulation of the supersaturation allowed the nucleation rate to be varied and led to the production of large crystals which were homogeneously distributed in the gel bead.

Protein crystallisation under microgravity conditions: What did we learn on TIM crystallisation from the Soyuz missions?

This study deals with heat transfer enhancement surface manufactured by thermal spraying. Two thermal spraying methods using copper as a coating material, wire flame spraying (WFS) and vacuum plasma spraying (VPS), were applied to the outside of copper cylinder with 20 mm OD. The surface structure by WFS was denser than that by VPS. The effect of gravity on boiling heat transfer coeffcient and wall superheat at the onset of boiling were experimentally evaluated under micro- and hyper-gravity condition during a parabolic trajectory flight of an airplane. Pool boiling experiments in saturated liquid of HCFC123 were carried out for heat fluxes between 1.0 and 160 kW/m2 and saturated temperature of 30 °C. As a result, the surface by VPS produced higher heat transfer coefficient and lower superheat at the onset of boiling under microgravity. For the smooth surface, the effect of gravity on boiling heat transfer coefficient was a little. For the coating, a large difference in heat transfer coefficient to gravity was observed in the moderate heat flux range. The heat transfer coefficinet decreased as gravity changed from the normal to hypergravity, and was improved as gravity changed from the hyperto microgravity. The difference in heat transfer coefficient between the normal and microgravity was a little. Heat transfer enhancement factor was kept over the experimental range of heat flux. It can be said that boiling behavior on thermal spray coating might be influenced by flow convection velocity.

Purification of an oxidation-sensitive enzyme, pI258 arsenate reductase from Staphylococcus aureus

Arsenate reductase (ArsC) from Staphylococcus aureus pI258 is extremely sensitive to oxidative inactivation. The presence of oxidized ArsC forms was not that critical for NMR, but kinetics and crystallization required an extra reversed-phase purification to increase sample homogeneity. The salt ions observed in the X-ray electron density of ArsC were investigated. Carbonate was found to have the lowest dissociation constant for activation (K(a)=1.1 mM) and potassium was stabilizing ArsC (DeltaT(m)=+6.2 degrees C). Also due to the use of these salt ions, the final yield of the purification had improved with a factor of four, i.e. 73 mg/l culture.

Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal domain of Ss-LrpB, a transcription regulator from Sulfolobus solfataricus.

Ss-LrpB from Sulfolobus solfataricus P2 belongs to the bacterial/archaeal superfamily of Lrp-like (leucine-responsive regulatory protein-like) transcription regulators. The N-terminal DNA-binding domain contains a HTH motif and the C-terminal domain contains an alphabeta-sandwich (betaalphabetabetaalphabeta fold). The C-terminal domain was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals belong to space group P2(1)2(1)2, with unit-cell parameters a = 59.35, b = 74.86, c = 38.08 A and a data set was collected to 2.0 A resolution. Structure determination using a selenomethionine derivative is under way.