issue contents

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983

April 2016 issue

Highlighted illustration

Cover illustration: The crystal structure of a Klebsiella pneumoniae topoisomerase IV ParC/ParE cleavage complex with DNA stabilized by levofloxacin (Veselkov et al., p. 488). The ParC subunit of the topoisomerase is shown in blue, the ParE subunit in yellow and DNA in cyan. Bound molecules of levofloxacin (a fluoroquinolone antibiotic) are shown in red. K. pneumoniae is a Gram-negative bacterium that is responsible for a range of common life-threatening infections and certain strains of Klebsiella have become highly resistant to antibiotics. In order to overcome this resistance, new drugs targeted against topoisomerase IV are being developed. The structure of the ParC/ParE-DNA-levofloxacin binding site highlights details that are essential for the rational design of Klebsiella topoisomerase inhibitors.

research papers



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Variants of the C—C bond-forming enzymes transaldolase B and D-fructose-6-phosphate aldolase A are irreversibly inhibited by D-tagatose 6-phosphate. A novel structure of a covalently bound ring sugar at the active-site lysine residue of the transaldolase B F178Y variant is revealed.

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The crystal structure of a 32-base-pair RNA double helix (675 non-H atoms) from a trypanosome RNA-editing substrate was determined with 1.05 Å resolution X-ray diffraction data starting from random phases using the direct-methods computer program SIR2014. Success was achieved in the presence of two levels of translational pseudosymmetry caused by three helical repeats.

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Crystal structures of the cleavage complexes of topoisomerase IV from Gram-negative (K. pneumoniae) and Gram-positive (S. pneumoniae) bacterial pathogens stabilized by the clinically important antibacterial drug levofloxacin are presented, analysed and compared. For K. pneumoniae, this is the first high-resolution cleavage complex structure to be reported.

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The first crystal structure of the RBM39-UHM–U2AF65-ULM complex has been determined at 2.2 Å resolution. Comparison to other UHM–ULM complexes reveals both common and unique interactions.

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A clear narrative of complex structure determination, including crystallographic problems of pseudo-merohedral twinning, pseudo-translational symmetry and data anisotropy, is provided. This manuscript provides a description of how these issues encountered during the structural determination of E. coli type I pyruvate kinase to 2.28 Å resolution were overcome.

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A liquid-droplet injector delivers microcrystals of lysozyme in a pulse-by-pulse manner for conducting serial femtosecond crystallography with an X-ray free-electron laser. The structure was determined at a resolution of 2.3 Å with low sample consumption.

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A new crystal structure of linear Ub2 reveals a more compact conformation than the previously known conformations. Solution conformations of linear Ub2, Ub3 and Ub4 were probed by small-angle X-ray scattering, revealing that linear Ub3 predominantly adopts compact conformations while linear Ub2 and Ub4 adopt an extended conformation. The results provide a full view of the conformational diversity of linear polyubiquitins.

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When crystallized in the absence of the allosteric inhibitor AMP, human muscle fructose-1,6-bisphosphatase has a totally unexpected quaternary structure of its active R form, with the two dimers of the homotetrameric molecule in a perpendicular orientation, in stark contrast to the coplanar arrangement of the closely related liver isozyme. The T-to-R switch of the muscle enzyme also involves a highly unusual α→β refolding of the N-terminus.

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Ancil structures correlated with the target structures are used to improve phases via the Phantom Derivative approach.

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A comprehensive description of the methods used within the DIALS framework for diffraction-geometry refinement using predicted reflection centroids is given. Examples of the advanced features of the software are provided.

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A streamlined pipeline for structure determination is described that applies in cellulo X-ray diffraction analysis to crystal-containing cells isolated by flow cytometry. Application of this pipeline to in vivo-grown crystals of the recombinant CPV1 polyhedrin shows that in cellulo analysis is more efficient, is compatible with experimental phasing and does not compromise the quality of the final model.

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XModeScore determines the correct protomeric/tautomeric state or mode of active-site residues along with any bound ligand(s) using quantum-mechanics-based X-ray refinement followed by post-refinement scoring based on a combination of energetic strain (or ligand strain) and rigorous difference electron-density analysis.

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