The crystal structure of alanine racemase from Streptococcus pneumoniae, a target for structure-based drug design

<p>Abstract</p> <p>Background</p> <p><it>Streptococcus pneumoniae </it>is a globally important pathogen. The Gram-positive diplococcus is a leading cause of pneumonia, otitis media, bacteremia, and meningitis, and antibiotic resistant strains have become increasingly common over recent years.Alanine racemase is a ubiquitous enzyme among bacteria and provides the essential cell wall precursor, D-alanine. Since it is absent in humans, this enzyme is an attractive target for the development of drugs against <it>S. pneumoniae </it>and other bacterial pathogens.</p> <p>Results</p> <p>Here we report the crystal structure of alanine racemase from <it>S. pneumoniae </it>(Alr_SP). Crystals diffracted to a resolution of 2.0 Å and belong to the space group P3₁21 with the unit cell parameters a = b = 119.97 Å, c = 118.10 Å, α = β = 90° and γ = 120°. Structural comparisons show that Alr_SPshares both an overall fold and key active site residues with other bacterial alanine racemases. The active site cavity is similar to other Gram positive alanine racemases, featuring a restricted but conserved entryway.</p> <p>Conclusions</p> <p>We have solved the structure of Alr_SP, an essential step towards the development of an accurate pharmacophore model of the enzyme, and an important contribution towards our on-going alanine racemase structure-based drug design project. We have identified three regions on the enzyme that could be targeted for inhibitor design, the active site, the dimer interface, and the active site entryway.</p

Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames)

<p>Abstract</p> <p>Background</p> <p><it>Bacillus anthracis </it>is the causative agent of anthrax and a potential bioterrorism threat. Here we report the biochemical and structural characterization of <it>B. anthracis </it>(Ames) alanine racemase (Alr_<it>Bax</it>), an essential enzyme in prokaryotes and a target for antimicrobial drug development. We also compare the native Alr_{<it>Bax </it>}structure to a recently reported structure of the same enzyme obtained through reductive lysine methylation.</p> <p>Results</p> <p><it>B. anthracis </it>has two open reading frames encoding for putative alanine racemases. We show that only one, <it>dal1</it>, is able to complement a D-alanine auxotrophic strain of <it>E. coli</it>. Purified Dal1, which we term Alr_<it>Bax</it>, is shown to be a dimer in solution by dynamic light scattering and has a V_maxfor racemization (L- to D-alanine) of 101 U/mg. The crystal structure of unmodified Alr_{<it>Bax </it>}is reported here to 1.95 Å resolution. Despite the overall similarity of the fold to other alanine racemases, Alr_{<it>Bax </it>}makes use of a chloride ion to position key active site residues for catalysis, a feature not yet observed for this enzyme in other species. Crystal contacts are more extensive in the methylated structure compared to the unmethylated structure.</p> <p>Conclusion</p> <p>The chloride ion in Alr_{<it>Bax </it>}is functioning effectively as a carbamylated lysine making it an integral and unique part of this structure. Despite differences in space group and crystal form, the two Alr_{<it>Bax </it>}structures are very similar, supporting the case that reductive methylation is a valid rescue strategy for proteins recalcitrant to crystallization, and does not, in this case, result in artifacts in the tertiary structure.</p

Unravelling the Role of the Pentafluoroorthotellurate Group as a Ligand in Nickel Chemistry

The pentafluoroorthotellurate group (teflate, OTeF5) is able to form species, for which only the fluoride analogues are known. Despite nickel fluorides being widely investigated, nickel teflates have remained elusive for decades. By reaction of [NiCl4]2− and neat ClOTeF5, we have synthesized the homoleptic [Ni(OTeF5)4]2− anion, which presents a distorted tetrahedral structure, unlike the polymeric [NiF4]2−. This high‐spin complex has allowed the study of the electronic properties of the teflate group, which can be classified as a weak/medium‐field ligand, and therefore behaves as the fluoride analogue also in ligand‐field terms. The teflate ligands in [NEt4]2[Ni(OTeF5)4] are easily substituted, as shown by the formation of [Ni(NCMe)6][OTeF5]2 by dissolving it in acetonitrile. Nevertheless, careful reactions with other conventional ligands have enabled the crystallization of nickel teflate complexes with different coordination geometries, i.e. [NEt4]2[trans‐Ni(OEt2)2(OTeF5)4] or [NEt4][Ni(bpyMe2)(OTeF5)3].Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Peer Reviewe

Unravelling the Role of the Pentafluoroorthotellurate Group as a Ligand in Nickel Chemistry

The pentafluoroorthotellurate group (teflate, OTeF5) is able to form species, for which only the fluoride analogues are known. Despite nickel fluorides being widely investigated, nickel teflates have remained elusive for decades. By reaction of [NiCl4]2− and neat ClOTeF5, we have synthesized the homoleptic [Ni(OTeF5)4]2− anion, which presents a distorted tetrahedral structure, unlike the polymeric [NiF4]2−. This high‐spin complex has allowed the study of the electronic properties of the teflate group, which can be classified as a weak/medium‐field ligand, and therefore behaves as the fluoride analogue also in ligand‐field terms. The teflate ligands in [NEt4]2[Ni(OTeF5)4] are easily substituted, as shown by the formation of [Ni(NCMe)6][OTeF5]2 by dissolving it in acetonitrile. Nevertheless, careful reactions with other conventional ligands have enabled the crystallization of nickel teflate complexes with different coordination geometries, i.e. [NEt4]2[trans‐Ni(OEt2)2(OTeF5)4] or [NEt4][Ni(bpyMe2)(OTeF5)3]

Purification and preliminary crystallization of alanine racemase from Streptococcus pneumoniae

<p>Abstract</p> <p>Background</p> <p>Over the past fifteen years, antibiotic resistance in the Gram-positive opportunistic human pathogen <it>Streptococcus pneumoniae </it>has significantly increased. Clinical isolates from patients with community-acquired pneumonia or otitis media often display resistance to two or more antibiotics. Given the need for new therapeutics, we intend to investigate enzymes of cell wall biosynthesis as novel drug targets. Alanine racemase, a ubiquitous enzyme among bacteria and absent in humans, provides the essential cell wall precursor, D-alanine, which forms part of the tetrapeptide crosslinking the peptidoglycan layer.</p> <p>Results</p> <p>The alanine racemases gene from <it>S. pneumoniae </it>(<it>alr</it>_<it>SP</it>) was amplified by PCR and cloned and expressed in <it>Escherichia coli</it>. The 367 amino acid, 39854 Da dimeric enzyme was purified to electrophoretic homogeneity and preliminary crystals were obtained. Racemic activity was demonstrated through complementation of an <it>alr </it>auxotroph of <it>E. coli </it>growing on L-alanine. In an alanine racemases photometric assay, specific activities of 87.0 and 84.8 U mg^-1were determined for the conversion of D- to L-alanine and L- to D-alanine, respectively.</p> <p>Conclusion</p> <p>We have isolated and characterized the alanine racemase gene from the opportunistic human pathogen <it>S. pneumoniae</it>. The enzyme shows sufficient homology with other alanine racemases to allow its integration into our ongoing structure-based drug design project.</p

Lack of evidence for xenotropic murine leukemia virus-related virus(XMRV) in German prostate cancer patients

Background: A novel gammaretrovirus named xenotropic murine leukemia virus-related virus (XMRV) has been recently identified and found to have a prevalence of 40% in prostate tumor samples from American patients carrying a homozygous R462Q mutation in the RNaseL gene. This mutation impairs the function of the innate antiviral type I interferon pathway and is a known susceptibility factor for prostate cancer. Here, we attempt to measure the prevalence of XMRV in prostate cancer cases in Germany and determine whether an analogous association with the R462Q polymorphism exists. Results: 589 prostate tumor samples were genotyped by real-time PCR with regard to the RNaseL mutation. DNA and RNA samples from these patients were screened for the presence of XMRV-specific gag sequences using a highly sensitive nested PCR and RT-PCR approach. Furthermore, 146 sera samples from prostate tumor patients were tested for XMRV Gag and Env antibodies using a newly developed ELISA assay. In agreement with earlier data, 12.9% (76 samples) were shown to be of the QQ genotype. However, XMRV specific sequences were detected at neither the DNA nor the RNA level. Consistent with this result, none of the sera analyzed from prostate cancer patients contained XMRV-specific antibodies. Conclusion: Our results indicate a much lower prevalence (or even complete absence) of XMRV in prostate tumor patients in Germany. One possible reason for this could be a geographically restricted incidence of XMRV infections

Subjektive Theorien und erfolgreiches Handeln von Lehrern/-innen bei Unterrichtskonflikten

Durch einen Vergleich zwischen erfolgreichen und weniger erfolgreichen Lehrern/-innen angesichts von Unterrichtskonflikten sollen Aufschlüsse über den Zusammenhang zwischen Subjektiven Theorien und interaktivem Handeln gewonnen werden. Gestützt auf unterschiedliche Indikatoren aus systematischer Unterrichtsbeobachtung, Expertenratings und Selbstbeurteilung der Lehrer/-innen werden zunächst grundlegende Dimensionen erfolgreichen Unterrichts im Hinblick auf die Konfliktbewältigung ermittelt und im einzelnen durch Merkmale des Schülerhandelns, des Lehrerhandelns und der Lehrer-Schüler-Interaktion beschrieben. Subjektive Theorien wurden teils mittels Fragebogen, v.a. aber mit der "Interview- und Legetechnik zur Rekonstruktion kognitiver Handlungsstrukturen" erhoben. Auf dieser Basis ergibt sich, daß erfolgreichere Lehrer/-innen verstärkt Variablen, die sie selbst beeinflussen können, als Ursachen für Schüleraggressionen in Betracht ziehen. Sie unterscheiden sich darüber hinaus von weniger erfolgreichen Lehrer/-innen in systematischer Weise in der Komplexität, Organisation und Handlungskonsistenz ihres subjektiv-theoretischen Herstellungswissens. (DIPF/Orig.)The intention of this article is to yield empirical insights into the relationship between subjective theories and goal-oriented actions through a comparison of teachers that differ in their ability to cope with conflicts during class hours. Basic dimensions of successful teaching concerning conflict management are developed on the basis of systematic observation, expert ratings and teachers\u27 self statements. These dimensions are described in detail in terms of students\u27 actions, teachers\u27 actions and teacher-student-interactions. Subjective theories have been reconstructed in part by questionnaire, but mainly through a special method using stimulated recall, interview, and graphic representation. Explaining students\u27 aggression, more successful teachers prefer factors which depend on their own behaviour. Moreover their subjective theories are different from those of less successful teachers in respect of complexity, organization, and consistency with overt behavior. Results are discussed in terms of action theory and cognitive functioning. (DIPF/Orig.

Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1

Pyrroline-5-carboxylate reductase (PYCR) is the final enzyme in proline biosynthesis, catalyzing the NAD(P)H-dependent reduction of [?]1-pyrroline-5-carboxylate (P5C) to proline. Mutations in the PYCR1 gene alter mitochondrial function and cause the connective tissue disorder cutis laxa. Furthermore, PYCR1 is overexpressed in multiple cancers, and the PYCR1 knock-out suppresses tumorigenic growth, suggesting that PYCR1 is a potential cancer target. However, inhibitor development has been stymied by limited mechanistic details for the enzyme, particularly in light of a previous crystallographic study that placed the cofactor-binding site in the C-terminal domain rather than the anticipated Rossmann fold of the N-terminal domain. To fill this gap, we report crystallographic, sedimentation- velocity, and kinetics data for human PYCR1. Structures of binary complexes of PYCR1 with NADPH or proline determined at 1.9 Å resolution provide insight into cofactor and substrate recognition.WeseeNADPHbound to the Rossmann fold, over 25 Å from the previously proposed site. The 1.85 Å resolution structure of a ternary complex containing NADPH and a P5C/proline analog provides a model of the Michaelis complex formed during hydride transfer. Sedimentation velocity shows that PYCR1 forms a concentration-dependent decamer in solution, consistent with the pentamer-of-dimers assembly seen crystallographically. Kinetic and mutational analysis confirmed several features seen in the crystal structure, including the importance of a hydrogen bond between Thr-238 and the substrate as well as limited cofactor discrimination

Gamma-Ray Emissions from Pulsars: Spectra of the TEV Fluxes from Outer-Gap Accelerators

We study the gamma-ray emissions from an outer-magnetospheric potential gap around a rotating neutron star. Migratory electrons and positrons are accelerated by the electric field in the gap to radiate copious gamma-rays via curvature process. Some of these gamma-rays materialize as pairs by colliding with the X-rays in the gap, leading to a pair production cascade. Imposing the closure condition that a single pair produces one pair in the gap on average, we explicitly solve the strength of the acceleration field and demonstrate how the peak energy and the luminosity of the curvature-radiated, GeV photons depend on the strength of the surface blackbody and the power-law emissions. Some predictions on the GeV emission from twelve rotation-powered pulsars are presented. We further demonstrate that the expected pulsed TeV fluxes are consistent with their observational upper limits. An implication of high-energy pulse phase width versus pulsar age, spin, and magnetic moment is discussed.Comment: Revised to compute absolute TeV spectra (22 pages, 9 figures