A cardioviral 2C-ATP complex structure reveals the essential role of a conserved arginine in regulation of cardioviral 2C activity.

Unlabelled: 2C is a highly conserved picornaviral non-structural protein with ATPase activity and plays a multifunctional role in the viral life cycle as a promising target for anti-picornavirus drug development. While the structure-function of enteroviral 2Cs have been well studied, cardioviral 2Cs remain largely uncharacterized. Here, an endogenous ATP molecule was identified in the crystal structure of 2C from encephalomyocarditis virus (EMCV, Cardiovirus A).

Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data.

Over the past decade, iterative projection algorithms, an effective approach to recovering phases from a single intensity measurement, have found application in protein crystallography to directly surmount the `phase problem'. However, previous studies have always assumed that some prior knowledge constraints (i.e.

Allosteric regulation of Senecavirus A 3Cpro proteolytic activity by an endogenous phospholipid.

Seneca virus A (SVA) is an emerging novel picornavirus that has recently been identified as the causative agent of many cases of porcine vesicular diseases in multiple countries. In addition to cleavage of viral polyprotein, the viral 3C protease (3Cpro) plays an important role in the regulation of several physiological processes involved in cellular antiviral responses by cleaving critical cellular proteins. Through a combination of crystallography, untargeted lipidomics, and immunoblotting, we identified the association of SVA 3Cpro with an endogenous phospholipid molecule, which binds to a unique region neighboring the proteolytic site of SVA 3Cpro.

Structural basis for the transformation of the traditional medicine berberine by bacterial nitroreductase.

The bacterial nitroreductases (NRs) NfsB and NfsA are conserved homodimeric FMN-dependent flavoproteins that are responsible for the reduction of nitroaromatic substrates. Berberine (BBR) is a plant-derived isoquinoline alkaloid with a large conjugated ring system that is widely used in the treatment of various diseases. It was recently found that the gut microbiota convert BBR into dihydroberberine (dhBBR, the absorbable form) mediated by bacterial NRs.

oligosaccharides increase serotonin in the brain and ameliorate depression promoting 5-hydroxytryptophan production in the gut microbiota.

oligosaccharides (MOO) are an oral drug approved in China for the treatment of depression in China. However, MOO is hardly absorbed so that their anti-depressant mechanism has not been elucidated. Here, we show that oral MOO acted on tryptophan → 5-hydroxytryptophan (5-HTP) → serotonin (5-HT) metabolic pathway in the gut microbiota.

Gut dysbacteriosis attenuates resistance to infection by decreasing cyclooxygenase 2 to inhibit endoplasmic reticulum stress.

The role of gut microbiota has been described as an important influencer of the immune system. Gut-lung axis is critical in the prevention of mycobacterium infection, but the specific mechanism, by which dysbiosis affects tuberculosis, has not been reported. In this study, we attempted to provide more information on how the gut-lung axis contributes to () infection.

Structural basis of a multi-functional deaminase in chlorovirus PBCV-1.

2-Deoxycytidylate deaminase (dCD) is a member of the zinc-dependent cytidine deaminase family features in its allosterically regulated mechanism by dCTP and dTTP. The large double-stranded DNA-containing chlorovirus PBCV-1 encodes a dCD family enzyme PBCV1dCD that was reported to be able to deaminize both dCMP and dCTP, which makes PBCV1dCD unique in the dCD family proteins. In this study, we report the crystal structure of PBCV1dCD in complex with dCTP/dCMP and dTTP/dTMP, respectively.

Mamba: a systematic software solution for beamline experiments at HEPS.

To cater for the diverse experiment requirements at the High Energy Photon Source (HEPS) with often limited human resources, Bluesky was chosen as the basis for our software framework, Mamba. In our attempt to address Bluesky's lack of integrated graphical user interfaces (GUIs), command injection with feedback was chosen as the main way for the GUIs to cooperate with the command line interface; a remote-procedure-call service is also provided, which covers functionalities unsuitable for command injection, as well as pushing of status updates. In order to fully support high-frequency applications like fly scans, Bluesky's support for asynchronous control is being improved; furthermore, to support high-throughput experiments, Mamba Data Worker is being developed to cover the complexity in asynchronous online data processing for these experiments.

Insights into the Neutralization and DNA Binding of Toxin-Antitoxin System ParE-CopA by Structure-Function Studies.

ParE-CopA is a new type II toxin-antitoxin (TA) system in prophage CP4So that plays an essential role in circular CP4So maintenance after the excision in . The toxin ParE severely inhibits cell growth, while CopA functions as an antitoxin to neutralize ParE toxicity through direct interactions. However, the molecular mechanism of the neutralization and autoregulation of the TA operon transcription remains elusive.

A reference-based multi-lattice indexing method integrating prior information correction and iterative refinement in protein crystallography.

A new multi-lattice indexing method based on the principle of whole-pattern matching given cell dimensions and space-group symmetry is presented for macromolecular crystallography. The proposed method, termed the multi-crystal data processing suite (MCDPS), features a local correction for prior information accompanied by iterative refinement of experimental parameters, both of which are numerically and experimentally demonstrated to be critical for accurately identifying multiple crystal lattices. Further analysis of data reduction and structure determination with conventional single-crystal programs reveals that the processed multi-lattice data sets are comparable in quality to typical single-crystal ones in terms of crystallographic metrics.

Structure and Biochemical Characteristic of the Methyltransferase (MTase) Domain of RNA Capping Enzyme from African Swine Fever Virus.

African swine fever virus (ASFV) is a complex nucleocytoplasmic large DNA virus (NCLDV) that causes a devastating swine disease and it is urgently needed to develop effective anti-ASFV vaccines and drugs. The process of mRNA 5'-end capping is a common characteristic in eukaryotes and many viruses, and the cap structure is required for mRNA stability and efficient translation. The ASFV protein pNP868R was found to have guanylyltransferase (GTase) activity involved in mRNA capping.

A micro-focusing and high-flux-throughput beamline design using a bending magnet for microscopic XAFS at the High Energy Photon Source.

An optical design study of a bending-magnet beamline, based on multi-bend achromat storage ring lattices, at the High Energy Photon Source, to be built in Beijing, China, is described. The main purpose of the beamline design is to produce a micro-scale beam from a bending-magnet source with little flux loss through apertures. To maximize the flux of the focal spot, the synchrotron source will be 1:1 imaged to a virtual source by a toroidal mirror; a mirror pair will be used to collimate the virtual source into quasi-parallel light which will be refocused by a Kirkpatrick-Baez mirror pair.

Conformational changes of antitoxin HigA from Escherichia coli str. K-12 upon binding of its cognate toxin HigB reveal a new regulation mechanism in toxin-antitoxin systems.

HigA functions as the antitoxin in HigB-HigA toxin-antitoxin system. It neutralizes HigB-mediated toxicity by forming a stable toxin-antitoxin complex. Here the crystal structure of isolated HigA from Escherichia coli str.

Structural characterization of the Imm52 family protein TsiT in Pseudomonas aeruginosa.

The bacterial type VI secretion system (T6SS) utilizes many toxic effectors to gain advantage over interbacterial competition and eukaryotic host infection. Meanwhile, the cognate immunity proteins of these effectors are employed to protect themselves from the virulence. TseT and TsiT form an effector-immunity (E-I) protein pair secreted by T6SS of Pseudomonas aeruginosa.

The crystal structure of KSHV ORF57 reveals dimeric active sites important for protein stability and function.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a γ-herpesvirus closely associated with Kaposi's sarcoma, primary effusion lymphoma and multicentric Castleman disease. Open reading frame 57 (ORF57), a viral early protein of KSHV promotes splicing, stability and translation of viral mRNA and is essential for viral lytic replication. Previous studies demonstrated that dimerization of ORF57 stabilizes the protein, which is critical for its function.

Structure-function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN-MNT toxin-antitoxin system.

Toxin-antitoxin (TA) loci in bacteria are small genetic modules that regulate various cellular activities, including cell growth and death. The two-gene module encoding a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and a cognate MNT (minimal nucleotidyltransferase) domain have been predicted to represent a novel type II TA system prevalent in archaea and bacteria. However, the neutralization mechanism and cellular targets of the TA family remain unclear.

Crystal structure of the putative cytoplasmic protein STM0279 (Hcp2) from Salmonella typhimurium.

STM0279 is a putative cytoplasmic protein from Salmonella typhimurium and was recently renamed haemolysin co-regulated protein 2 (Hcp2), with the neighbouring STM0276 being Hcp1. Both of them are encoded by the type VI secretion system (T6SS) of the Salmonella pathogenicity island 6 (SPI-6) locus and have high sequence identity. The Hcp proteins may function as a vital component of the T6SS nanotube and as a transporter and chaperone of diverse effectors from the bacterial T6SS.

Structural and SAXS analysis of Tle5-Tli5 complex reveals a novel inhibition mechanism of H2-T6SS in Pseudomonas aeruginosa.

Widely spread in Gram-negative bacteria, the type VI secretion system (T6SS) secretes many effector-immunity protein pairs to help the bacteria compete against other prokaryotic rivals, and infect their eukaryotic hosts. Tle5 and Tle5B are two phospholipase effector protein secreted by T6SS of Pseudomonas aeruginosa. They can facilitate the bacterial internalization process into human epithelial cells by interacting with Akt protein of the PI3K-Akt signal pathway.

Structural analysis of Pseudomonas aeruginosa H3-T6SS immunity proteins.

The Pseudomonas aeruginosa PldB protein is a transkingdom effector secreted by the Type VI Secretion System (T6SS). PA5088, PA5087, and PA5086 are three immunity proteins that can suppress the virulence of PldB. We report the crystal structures of PA5088 and PA5087 at 2.

Structural insights into the inhibition mechanism of bacterial toxin LsoA by bacteriophage antitoxin Dmd.

Bacteria have obtained a variety of resistance mechanisms including toxin-antitoxin (TA) systems against bacteriophages (phages), whereas phages have also evolved to overcome bacterial anti-phage mechanisms. Dmd from T4 phage can suppress the toxicities of homologous toxins LsoA and RnlA from Escherichia coli, representing the first example of a phage antitoxin against multiple bacterial toxins in known TA systems. Here, the crystal structure of LsoA-Dmd complex showed Dmd is inserted into the deep groove between the N-terminal repeated domain (NRD) and the Dmd-binding domain (DBD) of LsoA.

Structural basis for the interaction of BamB with the POTRA3-4 domains of BamA.

In Escherichia coli, the Omp85 protein BamA and four lipoproteins (BamBCDE) constitute the BAM complex, which is essential for the assembly and insertion of outer membrane proteins into the outer membrane. Here, the crystal structure of BamB in complex with the POTRA3-4 domains of BamA is reported at 2.1 Å resolution.

Crystal structures of the BsPif1 helicase reveal that a major movement of the 2B SH3 domain is required for DNA unwinding.

Pif1 helicases are ubiquitous members of the SF1B family and are essential for maintaining genome stability. It was speculated that Pif1-specific motifs may fold in specific structures, conferring distinct activities upon it. Here, we report the crystal structures of the Pif1 helicase from Bacteroides spp with and without adenosine triphosphate (ATP) analog/ssDNA.

Full-length structure of the major autolysin LytA.

LytA is responsible for the autolysis of many Streptococcus species, including pathogens such as S. pneumoniae, S. pseudopneumoniae and S.

A multiple-common-lines method to determine the orientation of snapshot diffraction patterns from single particles.

With the development of X-ray free-electron lasers (XFELs), it is possible to determine the three-dimensional structures of noncrystalline objects with coherent X-ray diffraction imaging. In this diffract-and-destroy mode, many snapshot diffraction patterns are obtained from the identical objects which are presented one by one in random orientations to the XFEL beam. Determination of the orientation of an individual object is essential for reconstruction of a three-dimensional structure.