Structural and biochemical analyses of the tetrameric carboxypeptidase S9Cfn from Fusobacterium nucleatum
As one of the most abundant bacteria in the human oral cavity, Fusobacterium nucleatum is closely involved in various oral diseases and is also a risk factor for other diseases. The peptidases of F. nucleatum can digest exogenous peptides into amino acids to satisfy its nutrient requirements. Here, a putative F.   nucleatum peptidase, termed S9Cfn, which belongs to the S9C peptidase family was identified. Enzymatic activity assays combined with mass-spectrometric analysis revealed that S9Cfn is a carboxypeptidase, but not an aminopeptidase as previously annotated. The crystal structure of the S9Cfn tetramer was solved at ...
Source: Acta Crystallographica Section D - November 17, 2021 Category: Biochemistry Authors: Wang, X. Cheng, M.-T. Chen, Z.-P. Jiang, Y.-L. Ge, Y.-S. Xia, R. Hou, W.-T. Tags: carboxypeptidases serine peptidases Fusobacterium nucleatum crystallography oral disease research papers Source Type: research

Helical filament structure of the DREP3 CIDE domain reveals a unified mechanism of CIDE-domain assembly
The cell-death-inducing DFF45-like effector (CIDE) domain is a protein-interaction module comprising ∼ 80 amino acids and was initially identified in several apoptotic nucleases and their regulators. CIDE-domain-containing proteins were subsequently identified among proteins involved in lipid metabolism. Given the involvement of CIDE-domain-containing proteins in cell death and lipid homeostasis, their structure and function have been intensively studied. Here, the head-to-tail helical filament structure of the CIDE domain of DNA fragmentation factor-related protein 3 (DREP3) is presented. The helical filament structure ...
Source: Acta Crystallographica Section D - November 11, 2021 Category: Biochemistry Authors: Lee, S.Y. Kwon, S. Ha, H.J. Lee, S.H. Park, H.H. Tags: apoptotic DNA fragmentation CIDE family crystal structure DREP3 higher-order structure research papers Source Type: research

Legionella effector LegA15/AnkH contains an unrecognized cysteine protease-like domain and displays structural similarity to LegA3/AnkD, but differs in host cell localization
Legionella pneumophila is a human pathogen that causes Legionnaires' disease, a severe form of pneumonia. It can be found in various aquatic environments ranging from cooling towers to ponds. In addition to causing disease in humans, it can also infect free-living amoebae commonly found in various aquatic environments. Once inside a human lung macrophage, it creates a niche called the Legionella-containing vacuole where it can evade phagolysosomal degradation and replicate. During infection, normal cellular functions are hijacked by proteins that are secreted by the pathogen, called bacterial effectors. Here, the structura...
Source: Acta Crystallographica Section D - November 11, 2021 Category: Biochemistry Authors: Chung, I.Y.W. Li, L. Cygler, M. Tags: Legionella pneumophila Legionnaires' disease effector proteins LegA15/AnkD virulence factors crystal structure research papers Source Type: research

Structural and thermodynamic insights into a novel Mg2+ – citrate-binding protein from the ABC transporter superfamily
This study reports crystal structures of an Mg2+ – citrate-binding protein (MctA) from the Gram-negative thermophilic bacterium Thermus thermophilus HB8 in both apo and holo forms in the resolution range 1.63 – 2.50   Å . Despite binding various divalent metal ions, MctA possesses the coordination geometry to bind its physiological metal ion, Mg2+. The results also suggest an extended subclassification of cluster D SBPs, which are known to bind and transport divalent-metal-ion-complexed citrate molecules. Comparative assessment of the open and closed conformations of the wild-type and mutant MctA proteins suggests a...
Source: Acta Crystallographica Section D - November 11, 2021 Category: Biochemistry Authors: Mandal, S.K. Kanaujia, S.P. Tags: Gram-negative bacteria Thermus thermophilus HB8 nucleotide-binding domain secondary transporters ABC transporters substrate-binding proteins symporters Mg2 metal ions citrate research papers Source Type: research

John D. Westbrook Jr (1957 – 2021)
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - November 1, 2021 Category: Biochemistry Authors: Zardecki, C. Burley, S.K. Tags: obituaries John Westbrook Source Type: research

The structure of natively iodinated bovine thyroglobulin
Thyroglobulin is a homodimeric glycoprotein that is essential for the generation of thyroid hormones in vertebrates. Upon secretion into the lumen of follicles in the thyroid gland, tyrosine residues within the protein become iodinated to produce monoiodotyrosine (MIT) and diiodotyrosine (DIT). A subset of evolutionarily conserved pairs of DIT (and MIT) residues can then engage in oxidative coupling reactions that yield either thyroxine (T4; produced from coupling of a DIT `acceptor' with a DIT `donor') or triiodothyronine (T3; produced from coupling of a DIT acceptor with an MIT donor). Although multiple iodotyrosine resi...
Source: Acta Crystallographica Section D - October 29, 2021 Category: Biochemistry Authors: Kim, K. Kopylov, M. Bobe, D. Kelley, K. Eng, E.T. Arvan, P. Clarke, O.B. Tags: cryoEM thyroglobulin thyroid hormone synthesis thyroxine research papers Source Type: research

Thyroxine hormones visualized by the cryo-EM structure of bovine thyroglobulin
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - October 29, 2021 Category: Biochemistry Authors: Turk, D. Gun č ar, G. Tags: iodine bovine thyroglobulin electron cryo-microscopy scientific commentaries Source Type: research

Data- and diversity-driven development of a Shotgun crystallization screen using the Protein Data Bank
Protein crystallization has for decades been a critical and restrictive step in macromolecular structure determination via X-ray diffraction. Crystallization typically involves a multi-stage exploration of the available chemical space, beginning with an initial sampling (screening) followed by iterative refinement (optimization). Effective screening is important for reducing the number of optimization rounds required, reducing the cost and time required to determine a structure. Here, an initial screen (Shotgun II) derived from analysis of the up-to-date Protein Data Bank (PDB) is proposed and compared with the previously ...
Source: Acta Crystallographica Section D - October 27, 2021 Category: Biochemistry Authors: Abrahams, G. Newman, J. Tags: data mining REMARK280 Protein Data Bank crystallization screens Shotgun research papers Source Type: research

Monitoring reversion of hepatitis C virus-induced cellular alterations by direct-acting antivirals using cryo soft X-ray tomography and infrared microscopy
Hepatitis C virus (HCV) is an enveloped RNA virus. One of the hallmarks of HCV infection is a rearrangement of the host cell membranes, known as the `membranous web'. Full-field cryo soft X-ray tomography (cryo-SXT) in the water-window energy range (284 – 543   eV) was performed on the MISTRAL beamline to investigate, in whole unstained cells, the morphology of the membranous rearrangements induced in HCV replicon-harbouring cells in conditions close to the living physiological state. All morphological alterations could be reverted by a combination of sofosbuvir/daclatasvir, which are clinically approved antivirals (di...
Source: Acta Crystallographica Section D - October 27, 2021 Category: Biochemistry Authors: Perez-Berna, A.J. Benseny-Cases, N. Rodr í guez, M.J. Valcarcel, R. Carrascosa, J.L. Gastaminza, P. Pereiro, E. Tags: cryo soft X-ray tomography hepatitis C virus direct-acting antivirals synchrotron-based infrared microscopy membranous web research papers Source Type: research

The future of biomolecular simulation in the pharmaceutical industry: what we can learn from aerodynamics modelling and weather prediction. Part 1. understanding the physical and computational complexity of in silico drug design
The predictive power of simulation has become embedded in the infrastructure of modern economies. Computer-aided design is ubiquitous throughout industry. In aeronautical engineering, built infrastructure and materials manufacturing, simulations are routinely used to compute the performance of potential designs before construction. The ability to predict the behaviour of products is a driver of innovation by reducing the cost barrier to new designs, but also because radically novel ideas can be piloted with relatively little risk. Accurate weather forecasting is essential to guide domestic and military flight paths, and th...
Source: Acta Crystallographica Section D - October 27, 2021 Category: Biochemistry Authors: Edwards, T. Foloppe, N. Harris, S.A. Wells, G. Tags: biomolecular simulation molecular docking in silico drug design pharmaceutical industry topical reviews Source Type: research

Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins
This study reports the crystal structures of SdgB and SdgA from S. aureus as well as multiple structures of SdgB in complex with its substrates (for example UDP, N-acetylglucosamine or SDR peptides), products (glycosylated SDR peptides) or phosphate ions. Together with biophysical and biochemical analyses, this structural work uncovered the novel mechanism by which SdgB and SdgA carry out the glycosyl-transfer process to the long SDR region in SDR proteins. SdgB undergoes dynamic changes in its structure such as a transition from an open to a closed conformation upon ligand binding and takes diverse forms, both as a homodi...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Kim, D.-G. Baek, I. Lee, Y. Kim, H. Kim, J.Y. Bang, G. Kim, S. Yoon, H.J. Han, B.W. Suh, S.W. Kim, H.S. Tags: glycosyltransferases SdgB SdgA serine – aspartate repeats crystal structure Staphylococcus aureus staphylococcal adhesion research papers Source Type: research

Crystallization, structural characterization and kinetic analysis of a GH26 β -mannanase from Klebsiella oxytoca KUB-CW2-3
β -Mannanase (EC 3.2.1.78) is an enzyme that cleaves within the backbone of mannan-based polysaccharides at β -1,4-linked d-mannose residues, resulting in the formation of mannooligosaccharides (MOS), which are potential prebiotics. The GH26 β -mannanase KMAN from Klebsiella oxytoca KUB-CW2-3 shares 49 – 72% amino-acid sequence similarity with β -mannanases from other sources. The crystal structure of KMAN at a resolution of 2.57   Å revealed an open cleft-shaped active site. The enzyme structure is based on a ( β / α )8-barrel architecture, which is a typical characteristic of clan A glycoside hydrolase enzymes...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Pongsapipatana, N. Charoenwattanasatien, R. Pramanpol, N. Nguyen, T.-H. Haltrich, D. Nitisinprasert, S. Keawsompong, S. Tags: β -mannanases Klebsiella oxytoca X-ray crystallography structural analysis mannooligosaccharides research papers Source Type: research

Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family
The SorC/DeoR family is a large family of bacterial transcription regulators that are involved in the control of carbohydrate metabolism and quorum sensing. To understand the structural basis of DNA recognition, structural studies of two functionally characterized SorC/DeoR family members from Bacillus subtilis were performed: the deoxyribonucleoside regulator bsDeoR and the central glycolytic genes regulator bsCggR. Each selected protein represents one of the subgroups that are recognized within the family. Crystal structures were determined of the N-terminal DNA-binding domains of bsDeoR and bsCggR in complex with DNA du...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Š oltysov á , M. Sieglov á , I. F á bry, M. Brynda, J. Š kerlov á , J. Ř ez á č ov á , P. Tags: SorC/DeoR family protein – DNA complexes transcription repressors Bacillus subtilis deoxyribonucleoside regulator bsDeoR gene regulator bsCggR carbohydrate catabolism research papers Source Type: research

Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking by Pseudomonas aeruginosa
The capability to obtain essential nutrients in hostile environments is a critical skill for pathogens. Under zinc-deficient conditions, Pseudomonas aeruginosa expresses a pool of metal homeostasis control systems that is complex compared with other Gram-negative bacteria and has only been partially characterized. Here, the structure and zinc-binding properties of the protein PA4063, the first component of the PA4063 – PA4066 operon, are described. PA4063 has no homologs in other organisms and is characterized by the presence of two histidine-rich sequences. ITC titration detected two zinc-binding sites with micromolar a...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Fiorillo, A. Battistoni, A. Ammendola, S. Secli, V. Rinaldo, S. Cutruzzol à , F. Demitri, N. Ilari, A. Tags: PA4063 periplasmic zinc trafficking Pseudomonas aeruginosa ferredoxin-like fold research papers Source Type: research

Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II – transducer complex
Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complem...
Source: Acta Crystallographica Section D - October 20, 2021 Category: Biochemistry Authors: Ryzhykau, Y.L. Vlasov, A.V. Orekhov, P.S. Rulev, M.I. Rogachev, A.V. Vlasova, A.D. Kazantsev, A.S. Verteletskiy, D.P. Skoi, V.V. Brennich, M.E. Pernot, P. Murugova, T.N. Gordeliy, V.I. Kuklin, A.I. Tags: membrane proteins two-component systems small-angle scattering ab initio modelling detergent belt oligomerization state sensory rhodopsin II – transducer complex Natronomonas pharaonis research papers Source Type: research