Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data. The new approach has been used for six challenging structure determinations, including the crystal structures of membrane proteins and macromolecular complexes that have evaded experts using other methods, and large structures from a 3.0 Å resolution F 1 -ATPase data set and a 4.5 Å resolution SecYEG–SecA complex data set. All of the models were automatically built by the method to R free values of between 28.9 and 39.9% and were free from the initial model bias.

Bradyrhizobium japonicum sorbitol dehydrogenase is NADH-dependent and is active at elevated temperatures. The best substrate is D-glucitol (a synonym for D-sorbitol), although L-glucitol is also accepted, giving it particular potential in industrial applications. Crystallization led to a hexagonal crystal form, with crystals diffracting to 2.9 Å resolution. In attempts to phase the data, a molecular-replacement solution based upon PDB entry 4nbu (33% identical in sequence to the target) was found. The solution contained one molecule in the asymmetric unit, but a tetramer similar to that found in other short-chain dehydrogenases, including the search model, could be reconstructed by applying crystallographic symmetry operations. The active site contains electron density consistent with D-glucitol and phosphate, but there was not clear evidence for the binding of NADH. In a search for the features that determine the thermostability of the enzyme, the Tm for the orthologue from Rhodobacter sphaeroides, for which the structure was already known, was also determined, and this enzyme proved to be considerably less thermostable. A continuous β-sheet is formed between two monomers in the tetramer of the B. japonicum enzyme, a feature not generally shared by short-chain dehydrogenases, and which may contribute to thermostability, as may an increased Pro/Gly ratio.

BACKGROUND:Tiered trauma team response may contribute to efficient in-hospital trauma triage by reducing the amount of resources required and by improving health outcomes. This study evaluates current practice of trauma team activation (TTA) in Dutch emergency departments (EDs).METHODS:A survey was conducted among managers of all 102 EDs in the Netherlands, using a semi-structured online questionnaire.RESULTS:Seventy-two questionnaires were analysed. Most EDs use a one-team system (68 %). EDs with a tiered-response receive more multi trauma patients (p < 0.01) and have more trauma team alerts per year (p < 0.05) than one-team EDs. The number of trauma team members varies from three to 16 professionals. The ED nurse usually receives the pre-notification (97 %), whereas the decision to activate a team is made by an ED nurse (46 %), ED physician (30 %), by multiple professionals (20 %) or other (4 %). Information in the pre-notification mostly used for trauma team activation are Airway-Breathing-Circulation (87 %), Glasgow Coma Score (90 %), and Revised Trauma Score (85 %) or Paediatric Trauma Score (86 %). However, this information is only available for 75 % of the patients or less. Only 56 % of the respondents were satisfied with their current in-hospital trauma triage system.CONCLUSIONS:Trauma team activation varies across Dutch EDs and there is room for improvement in the trauma triage system used, size of the teams and the professionals involved. More direct communication and more uniform criteria could be used to efficiently and safely activate a specific trauma team. Therefore, the implementation of a revised national consensus guideline is recommended.

BACKGROUND:Group 1 grass pollen allergens are a major cause of allergic disease. Specific immunotherapy involving controlled administration of allergens can be used as a disease-modifying treatment for such disease. Recombinant allergen variants with reduced IgE binding capacity may be used as component in such vaccines, as they may induce fewer treatment side effects than materials currently in use. A mutated variant of the immunodominant C-terminal domain of the group 1 grass pollen allergen Phl p 1 was recently established through an approach that used a set of human monoclonal IgE as a guide to identify mutations that disturbed IgE-allergen interactions. Further analysis of this domain is required to establish its potential for use in treatment.METHODS:GST-tagged wild-type and mutated C-terminal domains of Phl p 1 were produced in Escherichia coli TUNER(DE3). The products were purified by affinity chromatography on immobilized glutathione. GST was removed by enzymatic cleavage and tag-free products were purified by size exclusion chromatography. Products were assessed by SDS-PAGE, circular dichroism spectroscopy, differential scanning fluorimetry and dynamic light scattering. Rats were immunized with GST-tagged and tag-free mutated C-terminal domain of Phl p 1. Antigen-binding properties of induced antibodies were assessed by immunochemical analysis.RESULTS:The mutated domain has a structure very similar to that of the wild-type domain as determined by circular dichroism, but a reduced thermal stability. Immunization of rats demonstrates that this IgE-hyporeactive domain, despite its three sequence modifications (K8A, N11A, D55A), is able to induce antibodies that substantially block the binding of allergic subjects' IgE to the wild-type allergen.CONCLUSIONS:It is concluded that this IgE-hyporeactive molecule can be produced in folded form and that it is able to induce an antibody response that efficiently competes with IgE recognition of Phl p 1. These findings suggest that it, or a further evolved variant thereof, is a candidate for use as a component in specific immunotherapy against grass pollen allergy.

A gene in Bradyrhizobium japonicum USDA 110, annotated as a ribitol dehydrogenase (RDH), had 87 % sequence identity (97 % positives) to the N-terminal 31 amino acids of an L-glucitol dehydrogenase from Stenotrophomonas maltophilia DSMZ 14322. The 729-bp long RDH gene coded for a protein consisting of 242 amino acids with a molecular mass of 26.1 kDa. The heterologously expressed protein not only exhibited the main enantio selective activity with D-glucitol oxidation to D-fructose but also converted L-glucitol to D-sorbose with enzymatic cofactor regeneration and a yield of 90 %. The temperature stability and the apparent K m value for L-glucitol oxidation let the enzyme appear as a promising subject for further improvement by enzyme evolution. We propose to rename the enzyme from the annotated RDH gene (locus tag bll6662) from B. japonicum USDA as a D-sorbitol dehydrogenase (EC 1.1.1.14).

The nuclease domain of colicin E7 metallonuclease (NColE7) contains its active centre at the C-terminus. The mutant ΔN4-NColE7-C* - where the four N-terminal residues including the positively charged K446, R447 and K449 are replaced with eight residues from the GST tag - is catalytically inactive. The crystal structure of this mutant demonstrates that its overall fold is very similar to that of the native NColE7 structure. This implicates the stabilizing effect of the remaining N-terminal sequence on the structure of the C-terminal catalytic site and the essential role of the deleted residues in the mechanism of the catalyzed reaction. Complementary QM/MM calculations on the protein-DNA complexes support the less favourable cleavage by the mutant protein than by NColE7. Furthermore, a water molecule as a possible ligand for the Zn(2+)-ion is proposed to play a role in the catalytic process. These results suggest that the mechanism of the Zn(2+)-containing HNH nucleases needs to be further studied and discussed.

Rhamnogalacturonan I lyases (RGI lyases) (EC 4.2.2.-) catalyze cleavage of α-1,4 bonds between rhamnose and galacturonic acid in the backbone of pectins by β-elimination. In the present study, targeted improvement of the thermostability of a PL family 11 RGI lyase from Bacillus licheniformis (DSM 13/ATCC14580) was examined by using a combinatorial protein engineering approach exploring additive effects of single amino acid substitutions. These were selected by using a consensus approach together with assessing protein stability changes (PoPMuSiC) and B-factor iterative test (B-FIT). The second-generation mutants involved combinations of two to seven individually favorable single mutations. Thermal stability was examined as half-life at 60 °C and by recording of thermal transitions by circular dichroism. Surprisingly, the biggest increment in thermal stability was achieved by producing the wild-type RGI lyase in Bacillus subtilis as opposed to in Pichia pastoris; this effect is suggested to be a negative result of glycosylation of the P. pastoris expressed enzyme. A ~ twofold improvement in thermal stability at 60 °C, accompanied by less significant increases in T m of the enzyme mutants, were obtained due to additive stabilizing effects of single amino acid mutations (E434L, G55V, and G326E) compared to the wild type. The crystal structure of the B. licheniformis wild-type RGI lyase was also determined; the structural analysis corroborated that especially mutation of charged amino acids to hydrophobic ones in surface-exposed loops produced favorable thermal stability effects.

aMTA-SZTE Bioinorganic Chemistry Research Group, Dóm tér 7, H-6720 Szeged, Hungary bDepartment of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary. E-mail: gyurcsik@chem.u-szeged.hu; Fax: +36 62544340 cDepartment of Chemistry, Universitetsparken 5, 2100 Copenhagen, Denmark. E-mail: sine@chem.ku.dk; Fax: +45 35320322 dDepartment of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kgs. Lyngby, Denmark. eInstitute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic fNagata Special Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan

A novel Emericella nidulans endo-β-1,4-galactanase (EnGAL) demonstrates a strong capacity to generate high levels of very potent prebiotic oligosaccharides from potato pulp, a by-product of the agricultural potato-starch industry. EnGAL belongs to glycoside hydrolase family 53 and shows high (72.5%) sequence identity to an endo-β-1,4-galactanase from Aspergillus aculeatus. Diffraction data extending to 2.0 Å resolution were collected from a crystal of EnGAL grown from conditions containing 0.2 M zinc acetate. The crystal structure showed a high similarity between EnGAL and other endo-β-1,4-galactanases belonging to GH53. It also revealed 15 zinc ions bound to the protein, one of which is located in the active site, where it is coordinated by residues Glu136 and Glu246 which comprise the catalytic machinery. The majority of the zinc ions are located on the surface of the enzyme, in some cases with side chains from two different molecules as ligands, thus explaining why the presence of zinc ions was essential for crystallization.

The metallonuclease colicin E7 is a member of the HNH family of endonucleases. It serves as a bacterial toxin in Escherichia coli, protecting the host cell from other related bacteria and bacteriophages by degradation of their chromosomal DNA under environmental stress. Its cell-killing activity is attributed to the nonspecific nuclease domain (NColE7), which possesses the catalytic beta beta alpha-type metal ion-binding HNH motif at its C-terminus. Mutations affecting the positively charged amino acids at the N-terminus of NColE7 (444-576) surprisingly showed no or significantly reduced endonuclease activity [Czene et al. (2013), J. Biol. Inorg. Chem. 18, 309-321]. The necessity of the N-terminal amino acids for the function of the C-terminal catalytic centre poses the possibility of allosteric activation within the enzyme. Precise knowledge of the intramolecular interactions of these residues that affect the catalytic activity could turn NColE7 into a novel platform for artificial nuclease design. In this study, the N-terminal deletion mutant Delta N4-NColE7-C* of the nuclease domain of colicin E7 selected by E. coli was overexpressed and crystallized at room temperature by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 1.6 angstrom resolution and could be indexed and averaged in the trigonal space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 55.4, c = 73.1 angstrom. Structure determination by molecular replacement is in progress.

Trauma teams can be activated by emergency department (ED) staff to assess and treat a seriously injured patient optimally. Some EDs have one trauma team available, other EDs have two or more different trauma teams to activate, tailored to the needs of the incoming patient. The decision if a (full or modified) trauma team should be activated is mostly based on information provided by the emergency medical service (EMS) and is called in-hospital trauma triage. A system with a tiered response may contribute to the efficiency of the in-hospital trauma triage process by better resource allocation, improved cost containment and in terms of patient outcomes.

The enzymatic degradation of recalcitrant plant biomass is one of the key industrial challenges of the 21st century. Accordingly, there is a continuing drive to discover new routes to promote polysaccharide degradation. Perhaps the most promising approach involves the application of “cellulase-enhancing factors,” such as those from the glycoside hydrolase (CAZy) GH61 family. Here we show that GH61 enzymes are a unique family of copper-dependent oxidases. We demonstrate that copper is needed for GH61 maximal activity and that the formation of cellodextrin and oxidized cellodextrin products by GH61 is enhanced in the presence of small molecule redox-active cofactors such as ascorbate and gallate. By using electron paramagnetic resonance spectroscopy and single-crystal X-ray diffraction, the active site of GH61 is revealed to contain a type II copper and, uniquely, a methylated histidine in the copper's coordination sphere, thus providing an innovative paradigm in bioinorganic enzymatic catalysis.

We present here the first experimental evidence for bound substrate in the active site of a rhamnogalacturonan lyase belonging to family 4 of polysaccharide lyases, Aspergillus aculeatus rhamnogalacturonan lyase (RGL4). RGL4 is involved in the degradation of rhamnogalacturonan-I, an important pectic plant cell wall polysaccharide. Based on the previously determined wild-type structure, enzyme variants RGL4_H210A and RGL4_K150A have been produced and characterized both kinetically and structurally, showing that His210 and Lys150 are key active-site residues. Crystals of the RGL4_K150A variant soaked with a rhamnogalacturonan digest gave a clear picture of substrate bound in the −3/+3 subsites. The crystallographic and kinetic studies on RGL4, and structural and sequence comparison to other enzymes in the same and other PL families, enable us to propose a detailed reaction mechanism for the β-elimination on [-,2)-α-l-rhamno-(1,4)-α-d-galacturonic acid-(1,-]. The mechanism differs significantly from the one established for pectate lyases, in which most often calcium ions are engaged in catalysis.

Page s 18(ST0966 and ST2187) from Sulfolobus tokodaii (St) were overexpressed in E. coli, purified, and crystallized.The crystal structure of Ap-ThrRS-1 has been successfully determined at 2.3 Å resolution, as the first example.Ap-ThrRS-1 is a dimeric enzyme, the two identical subunits being associated to each other.Each subunit is composed of the two domains for the catalytic reaction and for the anticodon-binding, as expected.Their structures are similar to those of Ec-ThrRS.The amino acid residues essential for the catalysis and for the anticodon recognition are highly conserved at the positions and in the orientations.The essential editing domain of ThrRS is completely missing in Ap-ThrRS-1 as expected, suggesting the necessity of the second enzyme ThrRS-2 for editing.Since the N-terminal sequence of Ap-ThrRS-2 is similar to the sequence of the editing domain of Pa-ThrRS, Ap-ThrRS-2 is expected to catalyze de-aminoacylation of the misacylated serine moiety at the CCA terminus.

BLUF‐domain‐comprising photoreceptors sense blue light by utilizing FAD as a chromophore. The ycgF gene product of Escherichia coli is composed of a N‐terminal BLUF domain and a C‐terminal EAL domain, with the latter postulated to catalyze c‐di‐GMP hydrolysis. The linkage between these two domains involves a predominantly helical segment. Its role on the function of the YcgF photoreceptor domain was examined by characterizing BLUF domains with and without this segment and reconstituting them with either FAD, FMN or riboflavin. The stability of the light‐adapted state of the YcgF BLUF domain depends on the presence of this joining, helical segment and the adenosine diphosphate moiety of FAD. In contrast to other BLUF domains, two‐dimensional 1H,15N and one‐dimensional 1H NMR spectra of isotope‐labeled YcgF‐(1–137) revealed large conformational changes during reversion from the light‐ to the dark‐adapted state. Based on these results the function of the joining helix in YcgF during signal transfer and the role of the BLUF domain in regulating c‐di‐GMP levels is discussed.