Structural evidence for asymmetric ligand binding to transthyretin

Transthyretin represents a notable example of an amyloidogenic protein which undergoes misfolding, leading to a degenerative disease known as amyloidosis. Evidence is provided for significant conformational differences between the two thyroxine binding sites in solution, consistent with an asymmetric ligand-binding pattern. Rationalization of the structural basis of the observed asymmetry will aid in the design of new drugs effective as transthyretin stabilizers, with the prospect of their use in the pharmacological therapy of transthyretin amyloidosis.

Structural basis of Deerpox virus-mediated inhibition of apoptosis

Deerpox virus employs the cell-death inhibitor DPV022 to prevent premature host cell death by engaging pro-death Bcl-2 proteins via two independent ligand-binding sites as part of a domain-swapped Bcl-2 fold.

Detection of trans–cis flips and peptide-plane flips in protein structures

A method is presented to detect peptide bonds that need either a trans–cis flip or a peptide-plane flip.

Structural and adhesive properties of the long polar fimbriae protein LpfD from adherent-invasive Escherichia coli

The LpfD protein represents the tip adhesin of enterobacteriaceal long polar fimbriae (LPF), and LpfD from the adherent invasive E. coli strain LF82 directs LPF binding towards the intestinal epithelium and underlying tissue.

Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens

An alternative strategy for PEG sampling is suggested through the use of four newly defined PEG smears to enhance chemical space in reduced screens with a benefit towards protein crystallization.

Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism

The crystal structures of substrate and nucleotide bound propionate kinase and its site-directed mutants at a resolution of 1.8–2.0 Å are presented here. A probable catalytic mechanism is proposed which may be applicable to acetokinase family members.

The quaternary structure of the eukaryotic DNA replication proteins Sld7 and Sld3

Crystal structures of the eukaryotic DNA replication initiator Sld7 in complex with Sld3 from yeasts were determined. The quaternary structure of the Sld3–Sld7 complex appears to be suitable to activate two helicase molecules loaded onto replication origins in a head-to-head manner.

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns.

From deep TLS validation to ensembles of atomic models built from elemental motions

Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices.

A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens

A crystallographic cocktail screening campaign against 680 fragments revealed a binding hotspot in the structure of T. cruzi histidyl-tRNA synthetase.

Structure of the green fluorescent protein NowGFP with an anionic tryptophan-based chromophore

The three-dimensional structure of the green fluorescent protein NowGFP (a successor to Cerulean) with an anionic tryptophan-based chromophore and that of the photoconverted form NowGFP_conv are reported. The relationship between structure and photophysical characteristics is investigated.

An unexpected reactivity of the P₄₆₀ cofactor in hydroxylamine oxidoreductase

An unexpected reactivity is found in a unique haem moiety bound covalently to an oxidase.

The first crystal structure of a glycoside hydrolase family 17 β-1,3-glucanosyltransferase displays a unique catalytic cleft

The crystal structures of a novel glycoside hydrolase (GH) family 17 β-1,3-glucanosyltransferase from R. miehei (RmBgt17A) and two different substrate complexes have been solved at resolutions of 1.30, 2.30 and 2.27 Å, respectively. The first crystal structure of a GH family 17 β-1,3-glucanosyltransferase may be useful in studies of the catalytic mechanism of GH family 17 proteins and provides a basis for further enzymatic engineering or antifungal drug screening.

Three-dimensional structure of the human breast cancer resistance protein (BCRP/ABCG2) in an inward-facing conformation

The first three-dimensional structure of human ABCG2 in the absence of nucleotides and transported substrates has been determined at 2.0 nm resolution. In this state, ABCG2 is in an inward-facing conformation.

Structure of shikimate kinase, an in vivo essential metabolic enzyme in the nosocomial pathogen Acinetobacter baumannii, in complex with shikimate

Shikimate kinase was determined to be essential for the growth and survival of A. baumannii in a rat soft-tissue infection model. The crystal structure of this enzyme in complex with shikimate and sulfate ion was determined to 1.91 Å resolution, revealing ligand-induced conformational changes of key motifs.

Structural and biophysical characterization of the α-carbonic anhydrase from the gammaproteobacterium Thiomicrospira crunogena XCL-2: insights into engineering thermostable enzymes for CO₂ sequestration

The crystal structure of the α-carbonic anhydrase (α-CA) from the gammaproteobacterium T. crunogena XCL-2 has been determined to 2.6 Å resolution and reveals features that provide it with thermal and pH stability that are not seen in human α-CAs.

Fully automatic characterization and data collection from crystals of biological macromolecules

A fully automatic system has been developed that performs X-ray centring and characterization of, and data collection from, large numbers of cryocooled crystals without human intervention.

Structure of the DNA-binding domain of the response regulator SaeR from Staphylococcus aureus

SaeR can bind to P1 promoter DNA using the canonical winged helix–turn–helix module.

Combining `dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography

In order to accelerate ligand screening using X-ray crystallography, the combination of in situ diffraction with pre-coating of 96-well crystallization plates using a DMSO stock solution of putative ligands before performing protein crystallization is proposed.