Covering complete proteomes with X-ray structures: a current snapshot

The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the `protein universe' are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins.

Anchoring protein crystals to mounting loops with hydrogel using inkjet technology

A method to fix protein crystals to mounting loops with hydro-gel using inkjet technology has been developed. The method allows soaking of the mounted crystals in ligand-containing solution and assists in the design of an automated drug-screening pipeline.

Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape

H. pylori Csd4 (HP1075), together with other peptidoglycan hydrolases, plays an important role in determining the helical cell shape. Its crystal structure has been determined in three different forms.

Anthrax toxin lethal factor domain 3 is highly mobile and responsive to ligand binding

Peptide substrates and small-molecule inhibitors bind anthrax toxin lethal factor in the space between domains 3 and 4 of the hydrolase. Domain 3 is attached on a hinge to domain 2 and can move through an angular arc of more than 35° in response to the binding of different ligands.

Insights into the relationship between the haem-binding pocket and the redox potential of c₆ cytochromes: four atomic resolution structures of c₆ and c₆-like proteins from Synechococcus sp. PCC 7002

Atomic resolution structures of cytochromes c₆ and c_6C from Synechococcus sp. PCC 7002 as well as their haem-pocket point mutants are presented. The biophysical and structural properties of these proteins have been characterized with particular focus on the relationship between the structure of the haem-binding pocket and the redox potential.

Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity

The structures of sperm whale myoglobin variants show that longer distances between the heme axial water and the distal histidine (i.e. weaker hydrogen bonds) correlate with stronger peroxidase activity.

The structural basis of urea-induced protein unfolding in β-catenin

Although urea and guanidine hydrochloride are commonly used to denature proteins, the molecular underpinnings of this process have remained unclear for a century. To address this question, crystal structures of β-catenin were determined at various urea concentrations.

Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli

Hydroperoxides are reactive oxygen species (ROS) that are toxic to all cells. This study presents the crystallographic structures of the Escherichia coli alkylhydroperoxides reductase (AhpR) subunits AhpC and AhpF and describes a novel overall mechanistic model of AhpR.

Structure of mouse muskelin discoidin domain and biochemical characterization of its self-association

The structure of the discoidin domain from mouse muskelin has been determined and analysis of the interdomain interaction suggests a mechanism for self-association.

Enzyme–substrate complex structures of CYP154C5 shed light on its mode of highly selective steroid hydroxylation

Four enzyme–substrate complex structures of CYP154C5 from N. farcinica with the steroids pregnenolone, progesterone, androstenedione and testosterone bound in the active site of the enzyme are reported, revealing structural determinants for the high regioselectivity and stereoselectivity of CYP154C5 in steroid hydroxylation.

Temperature-dependent radiation sensitivity and order of 70S ribosome crystals

The rate of global radiation damage to 70S ribosome crystals has been measured at 100, 180 and 300 K. At 100 and 300 K, damage rates are comparable to and much larger than those of model proteins, respectively. The larger damage rates at 300 K cannot explain the dramatically higher diffraction quality observed at 100 K.

Structural insights into the human RyR2 N-terminal region involved in cardiac arrhythmias

X-ray and solution structures of the human RyR2 N-terminal region were obtained under near-physiological conditions. The structure exhibits a unique network of interactions between its three domains, revealing an important stabilizing role of the central helix.

Effect of the L499M mutation of the ascomycetous Botrytis aclada laccase on redox potential and catalytic properties

The structures of the ascomycetous B. aclada laccase and its L499M T1-site mutant have been solved at 1.7 Å resolution. The mutant enzyme shows a 140 mV lower redox potential of the type 1 copper and altered kinetic behaviour. The wild type and the mutant have very similar structures, which makes it possible to relate the changes in the redox potential to the L499M mutation

Structure of ADC-68, a novel carbapenem-hydrolyzing class C extended-spectrum β-lactamase isolated from Acinetobacter baumannii

The crystal structure of ADC-68 reveals new mechanisms for expanding its substrate spectrum to extended-spectrum cephalosporins and carbapenems.

Structural characterization of the virulence factor nuclease A from Streptococcus agalactiae

Nuclease A (NucA) is an extracellular nuclease secreted from S. agalactiae and is required for full virulence during infection. Crystal structures and biochemical characterization of NucA mutants reveal possible roles for surface residues in DNA substrate binding and catalysis. These results may serve as a foundation for the design of targeted antibacterial therapeutic compounds.

A novel member of glycoside hydrolase family 30 subfamily 8 with altered substrate specificity

A GH30 subfamily 8 (GH30-8) xylanase with functional properties different from the canonical GH30-8 glucuronoxylan xylanohydrolases has been biochemically and structurally characterized. The findings highlight the diversity of xylanolytic activities that derive from the GH30 family of glycoside hydrolases.

Ligand-dependent active-site closure revealed in the crystal structure of Mycobacterium tuberculosis MenB complexed with product analogues

Mycobacterium tuberculosis MenB, or 1, 4-dihydroxynaphthoyl coenzyme A synthase, is found to undergo induced-fit conformational changes that play an important role in substrate recognition and catalytic mechanism.

Structural insights into the substrate specificity and transglycosylation activity of a fungal glycoside hydrolase family 5 β-mannosidase

The crystal structures of a first fungal glycoside hydrolase family 5 β-mannosidase from Rhizomucor miehei (RmMan5B) and of its inactive E202A mutant in complex with mannobiose, mannotriose and mannosyl-fructose are presented. Structural analyses reveal the structural basis of substrates binding.

Small-angle neutron scattering reveals the assembly mode and oligomeric architecture of TET, a large, dodecameric aminopeptidase

The present work illustrates that small-angle neutron scattering, deuteration and contrast variation, combined with in vitro particle reconstruction, constitutes a very efficient approach to determine subunit architectures in large, symmetric protein complexes. In the case of the 468 kDa heterododecameric TET peptidase machine, it was demonstrated that the assembly of the 12 subunits is a highly controlled process and represents a way to optimize the catalytic efficiency of the enzyme.

Structure–specificity relationships in Abp, a GH27 β-L-arabino­pyranosidase from Geobacillus stearothermophilus T6

The three-dimensional structure of the GH27 arabinopyranosidase (Abp) from G. stearothermophilus T6 has been determined by molecular replacement, leading to full structural analysis of wild-type Abp (at 2.28 Å resolution) and its catalytic mutant Abp-D197A with (at 2.20 Å resolution) and without (at 2.30 Å resolution) a bound L-arabinose product. The structures demonstrate that Abp is a tetramer built of two pincer-like dimers, as also confirmed by SAXS.

Structure of the gas vesicle protein GvpF from the cyanobacterium Microcystis aeruginosa

A novel protein fold and the first crystal structure of a gas vesicle protein are described.

Structure-based identification of inositol polyphosphate 1-phosphatase from Entamoeba histolytica

EhIPPase is probably the inositol polyphosphate 1-phosphatase of E. histolytica.

Alliin is a suicide substrate of Citrobacter freundii me­thionine γ-lyase: structural bases of inactivation of the enzyme

The structural bases of the inactivation of methionine γ-lyase by a new suicide substrate were determined.

Enzyme–adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface

The enzyme–adenylate structure of a bacterial ATP-dependent DNA ligase (ADL), which does not have any additional DNA-binding domains, is similar to minimal viral ADLs that comprise only the core catalytic domains. The bacterial ADL also lacks the unstructured loops which are involved in DNA binding in the viral ADLs, implying that it must instead use short well structured motifs of the core domains to engage its substrate.

Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N⁵)-carboxyamino­imidazole ribonucleotide synthase (PurK) from Bacillus anthracis

The first structure of B. anthracis PurK with a bicarbonate ion in the active site is reported. Based on several enzyme structures with different ligands in the active site, a mechanism for the enzymatic reaction is proposed.

Structural and functional characterization of an arylamine N-acetyltransferase from the pathogen Mycobacterium abscessus: differences from other mycobacterial isoforms and implications for selective inhibition

Arylamine N-acetyltransferases (NAT) are xenobiotic metabolizing-enzymes that can acetylate aromatic amine antibiotics. The structure of NAT from the pathogen Mycobacterium abscessus is reported and shows differences with other mycobacterial isoforms.

Structure of the OsSERK2 leucine-rich repeat extracellular domain

SERK proteins play a central role in immune and developmental signaling pathways in plants. Structural studies have been performed in order to better understand the role of the OsSERK2 coreceptor in signaling with its partner receptors. Here, crystal structures of the LRR domains of OsSERK2 and a D128N OsSERK2 mutant, expressed as hagfish variable lymphocyte receptor (VLR) fusions, are reported.

Structures of SAICAR synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg²⁺, AIR and Asp. Corrigendum

A correction is made to the article by Wolf et al. [(2014), Acta Cryst. D70, 841–850].