Acta crystallographica. Section F, Structural biology communications最新文献

We describe a device and a method for changing the ambient solution of a macromolecular crystal. The approach is gentle, automated, inexpensive and open source. Examples are given of the equilibration of three different crystals to new solutions with exchange times ranging from 5 to 180 min. In each case direct transfer of the crystal to the new solution causes cracking, which is eliminated with gradient equilibration using the described device. Crystals equilibrated with the device produce high-quality diffraction that yields refined structures comparable to those determined previously. The device offers a more systematic and labor-saving workflow than current practice both for performing diffraction analysis of macromolecular crystals and for investigating the response of macromolecular crystals to changes in solution composition.

Human mitochondrial manganese superoxide dismutase (MnSOD) converts superoxide into hydrogen peroxide and molecular oxygen, serving as a key defence against oxidative damage. Despite extensive studies, the full structural characterization of H₂O₂-binding sites in MnSOD remains largely unexplored. Previous H₂O₂-soaked MnSOD structures have identified two distinct H₂O₂-binding sites: one directly ligated to the catalytic manganese (LIG position) and another at the active-site gateway (PEO position) between the second-shell residues Tyr34 and His30. In this study, a kinetically impaired Gln143Asn MnSOD variant is used to trap and explore additional H₂O₂-binding sites beyond the second-shell solvent gate. In the wild-type enzyme, Gln143 mediates proton transfers with the manganese-bound solvent (WAT1) to drive redox cycling of the metal, which is necessary for effective superoxide dismutation. Substitution with Asn stalls catalysis because the increased distance from WAT1 disrupts critical proton-coupled electron-transfer (PCET) events, and the redox cycling of the active-site metal is impaired. This, in turn, stalls the electrostatic cycling of positive charge on the enzyme surface and enhances the likelihood of trapping transient H₂O₂-bound states in this variant. The results reveal several H₂O₂ molecules leading up to the active site, in addition to the canonical LIG and PEO positions.

Fucoidan is a complex, sulfated polysaccharide primarily found in brown algae, where it plays important structural and protective roles. Due to its abundance in marine ecosystems, many marine bacteria have evolved diverse and specialized enzymatic systems to degrade fucoidan, although the functions and structures of many of these enzymes remain uncharacterized. Here, we describe the structure of a newly identified fucosidase, FucWf4, which cleaves terminal, unsulfated fucose residues from linear, sulfated fucoidan. FucWf4 does not belong to any known glycoside hydrolase (GH) family, but shows the greatest similarity to GH29 fucosidases. We present the first crystal structure of FucWf4 in complex with fucose, revealing a unique C-terminal domain that resembles a carbohydrate-binding module, although it may have lost its carbohydrate-binding capacity and is absent from canonical GH29 enzymes. Docking experiments suggest the presence of a −1 subsite containing a potential sulfate-binding pocket, which may underlie the substrate specificity of the enzyme. Furthermore, sequence analysis of FucWf4 homologs reveals two distinct clades, likely corresponding to functionally divergent groups. Together, these findings provide new insights into the molecular basis of fucoidan recognition and degradation by this novel enzyme subfamily, laying the groundwork for future functional and structural studies.

Ketohexokinase (KHK) catalyses the initial step in fructose metabolism, converting the furanose form of d-fructose to fructose 1-phosphate in an ATP-dependent reaction. Given its central role in metabolic pathways, KHK has emerged as a target for pharmacological intervention in the treatment of non-alcoholic fatty liver disease, metabolic syndrome, type 2 diabetes and obesity. KHK exists as two isoforms, A and C, which arise from alternative splicing of exon 3, resulting in a differing 45-amino-acid sequence within the 298-amino-acid primary structure of the enzyme. KHK is a biological homodimer, with each subunit adopting an α/β-fold architecture that interlocks with a β-clasp domain. In the case of KHK-C at least two distinct conformations of the β-clasp domain have been identified, whereas this conformational flexibility had not been observed in KHK-A. Here, X-ray crystallographic structural investigations of unliganded murine KHK-A refined to 1.37 Å resolution revealed the adoption of two conformations similar to those adopted by the human ortholog, suggesting that this structural feature is conserved across species. The functional significance of these conformational changes in KHK-A is of particular interest as this isoform has been implicated in cancer metastasis through a `moonlighting' protein kinase activity. Understanding the mechanistic role of conformational shifts in KHK-A may provide insights into its broader physiological functions and therapeutic potential.

Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated data sets. Being able to easily access and utilize these is crucial to allow researchers to make optimal use of their research effort. The tools presented here are useful for collating existing public cryoEM data sets and/or creating new synthetic cryoEM data sets to aid the development of novel data processing and interpretation algorithms. In recent years, structural biology has seen the development of a multitude of machine-learning-based algorithms to aid numerous steps in the processing and reconstruction of experimental data sets and the use of these approaches has become widespread. Developing such techniques in structural biology requires access to large data sets, which can be cumbersome to curate and unwieldy to make use of. In this paper, we present a suite of Python software packages, which we collectively refer to as PERC (profet, EMPIARreader and CAKED). These are designed to reduce the burden which data curation places upon structural biology research. The protein structure fetcher (profet) package allows users to conveniently download and cleave sequences or structures from the Protein Data Bank or AlphaFold databases. EMPIARreader allows lazy loading of Electron Microscopy Public Image Archive data sets in a machine-learning-compatible structure. The Class Aggregator for Key Electron-microscopy Data (CAKED) package is designed to seamlessly facilitate the training of machine-learning models on electron microscopy data, including electron-cryo-microscopy-specific data augmentation and labeling. These packages may be utilized independently or as building blocks in workflows. All are available in open-source repositories and designed to be easily extensible to facilitate more advanced workflows if required.

The focused issue on the SAMPREP workshop is introduced. The virtual issue is available at https://journals.iucr.org/special_issues/2025/samprep23/.

The enzyme d-aspartate oxidase (DDO) oxidizes acidic d-amino acids using the coenzyme flavin adenine dinucleotide to generate the corresponding α-keto acids and ammonia. DDO differs from d-amino-acid oxidase (DAAO), which acts on neutral and basic d-amino acids. Although the enzymatic properties of DDO have been characterized in several species, the structure of DDO had remained unclear. The structure of DDO derived from Cryptococcus humicola strain UJ1 (chDDO) was determined by X-ray crystallography at 1.70 Å resolution. While the three-dimensional structures of DAAOs are known to be homodimers, chDDO forms a homotetramer. This difference was found to be caused by the deletion of one loop and the insertion of two loops.