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Structural Biology Planet

December 15, 2017

Articles in Acta Cryst F

Structure of the mouse acidic amino-acid decarboxylase GADL1

The structure of the mouse glutamic acid decarboxylase-like protein 1 (GADL1) is described. The structure gives new insights into the function of GADL1 and related decarboxylases.

by Raasakka et al. at December 15, 2017 08:12 AM

Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis

The cloning, purification, biophysical characterization, crystallization and X-ray diffraction analysis of the two periplasmic domains of N. meningitidis DsbD, a disulfide reductase essential for the viability of this human pathogen, are reported.

by Smith et al. at December 15, 2017 08:12 AM

Structure and stability of the Human respiratory syncytial virus M2–1 RNA-binding core domain reveals a compact and cooperative folding unit

A high-resolution crystal structure of the M2–1 RNA-binding domain of Human syncytial respiratory virus was determined. A combination of crystallography and SAXS indicated its role in C-terminal extension.

by Molina et al. at December 15, 2017 08:12 AM

Structure of aspartate β-semialdehyde dehydrogenase from Francisella tularensis

The crystal structure of aspartate β-semialdehyde dehydrogenase from F. tularensis has been determined.

by Mank et al. at December 15, 2017 08:12 AM

Current papers in Acta Cryst F

The novel thermostable cellulose-degrading enzyme DtCel5H from Dictyoglomus thermophilum: crystallization and X-ray crystallographic analysis

Cellulose-based products constitute the great majority of municipal waste, and applications of cellulases in the conversion of waste biomass to biofuels will be a key technology in future biorefineries. Currently, multi-enzymatic pre-treatment of biomass is a crucial step in making carbohydrates more accessible for subsequent fermentation. Using bioinformatics analysis, endo-β-(1,4)-glucanase from Dictyoglomus thermophilum (DtCel5H) was identified as a new member of glycosyl hydrolase family 5. The gene encoding DtCel5H was cloned and the recombinant protein was overexpressed for crystallization and biophysical studies. Here, it is shown that this enzyme is active on cellulose substrates and is highly thermostable. Crystals suitable for crystallographic investigations were also obtained in different crystallization conditions. In particular, ordered crystals of DtCel5H were obtained using either ammonium sulfate or polyethylene glycol (PEG) as a precipitant agent. The crystals obtained in the presence of ammonium sulfate belonged to space group P32, with unit-cell parameters a = 73.1, b = 73.1, 73.1, c = 127.8 Å, and diffracted to 1.5 Å resolution, whereas the second crystal form belonged to the orthorhombic space group P212121, with unit-cell parameters a = 49.3, b = 67.9, c = 103.7 Å, and diffracted to 1.6 Å resolution. The crystal structure was solved in both space groups using molecular-replacement methods. Structure–activity and structure–stability studies of DtCel5H will provide insights for the design of high-performance enzymes.

by Ruggiero, A. at December 15, 2017 08:12 AM

Crystal structure of cytoplasmic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae

Thiolases are vital enzymes which participate in both degradative and biosynthetic pathways. Biosynthetic thiolases catalyze carbon–carbon bond formation by a Claisen condensation reaction. The cytoplasmic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae, ERG10, catalyses carbon–carbon bond formation in the mevalonate pathway. The structure of a S. cerevisiae biosynthetic thiolase has not previously been reported. Here, crystal structures of apo ERG10 and its Cys91Ala variant were solved at resolutions of 2.2 and 1.95 Å, respectively. The structure determined shows that ERG10 shares the characteristic thiolase superfamily fold, with a similar active-site architecture to those of type II thiolases and a similar binding pocket, apart from Ala159 at the entrance to the pantetheine-binding cavity, which appears to be a determinant of the poor binding ability of the substrate. Moreover, comparative binding-pocket analysis of molecule B in the asymmetric unit of the apo structure with that of the CoA-bound complex of human mitochondrial acetoacetyl-CoA thiolase indicates the canonical binding mode of CoA. Furthermore, the steric hindrance revealed in a structural comparison of molecule A with the CoA-bound form raise the possibility of conformational changes that are associated with substrate binding.

by Niu, L at December 15, 2017 08:12 AM

Structure of aspartate β-semialdehyde dehydrogenase from Francisella tularensis

Aspartate β-semialdehyde dehydrogenase (ASADH) is an enzyme involved in the diaminopimelate pathway of lysine biosynthesis. It is essential for the viability of many pathogenic bacteria and therefore has been the subject of considerable research for the generation of novel antibiotic compounds. This manuscript describes the first structure of ASADH from Francisella tularensis, the causative agent of tularemia and a potential bioterrorism agent. The structure was determined at 2.45 Å resolution and has a similar biological assembly to other bacterial homologs. ASADH is known to be dimeric in bacteria and have extensive interchain contacts, which are thought to create a half-sites reactivity enzyme. ASADH from higher organisms shows a tetrameric oligomerization, which also has implications for both reactivity and regulation. This work analyzes the apo form of F. tularensis ASADH, as well as the binding of the enzyme to its cofactor NADP+.

by Chruszcz, M. at December 15, 2017 08:12 AM

Structure and stability of the Human respiratory syncytial virus M2–1 RNA-binding core domain reveals a compact and cooperative folding unit

Human syncytial respiratory virus is a nonsegmented negative-strand RNA virus with serious implications for respiratory disease in infants, and has recently been reclassified into a new family, Pneumoviridae. One of the main reasons for this classification is the unique presence of a transcriptional antiterminator, called M2–1. The puzzling mechanism of action of M2–1, which is a rarity among antiterminators in viruses and is part of the RNA polymerase complex, relies on dissecting the structure and function of this multidomain tetramer. The RNA-binding activity is located in a monomeric globular `core' domain, a high-resolution crystal structure of which is now presented. The structure reveals a compact domain which is superimposable on the full-length M2–1 tetramer, with additional electron density for the C-terminal tail that was not observed in the previous models. Moreover, its folding stability was determined through chemical denaturation, which shows that the secondary and tertiary structure unfold concomitantly, which is indicative of a two-state equilibrium. These results constitute a further step in the understanding of this unique RNA-binding domain, for which there is no sequence or structural counterpart outside this virus family, in addition to its implications in transcription regulation and its likeliness as an antiviral target.

by Tidow, H. at December 15, 2017 12:00 AM