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Structural Biology Planet

September 21, 2018

Current papers in Acta Cryst F

Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence

ERG3 (ETS-related gene) is a member of the ETS (erythroblast transformation-specific) family of transcription factors, which contain a highly conserved DNA-binding domain. The ETS family of transcription factors differ in their binding to promoter DNA sequences, and the mechanism of their DNA-sequence discrimination is little known. In the current study, crystals of the ETSi domain (the ETS domain of ERG3 containing a CID motif) in space group P41212 and of its complex with the E74 DNA sequence (DNA9) in space group C2221 were obtained and their structures were determined. Comparative structure analysis of the ETSi domain and its complex with DNA9 with previously determined structures of the ERGi domain (the ETS domain of ERG containing inhibitory motifs) in space group P65212 and of the ERGi–DNA12 complex in space group P41212 were performed. The ETSi domain is observed as a homodimer in solution as well as in the crystallographic asymmetric unit. Superposition of the structure of the ETSi domain on that of the ERGi domain showed a major conformational change at the C-terminal DNA-binding autoinhibitory (CID) motif, while minor changes are observed in the loop regions of the ETSi-domain structure. The ETSi–DNA9 complex in space group C2221 forms a structure that is quite similar to that of the ERG–DNA12 complex in space group P41212. Upon superposition of the complexes, major conformational changes are observed at the 5′ and 3′ ends of DNA9, while the conformation of the core GGA nucleotides was quite conserved. Comparison of the ETSi–DNA9 structure with known structures of ETS class 1 protein–DNA complexes shows the similarities and differences in the promoter DNA binding and specificity of the class 1 ETS proteins.

by Saxena, A.K. at September 21, 2018 12:00 AM

Re-refinement of Plasmodium falciparum orotidine 5′-monophosphate decarboxylase provides a clearer picture of an important malarial drug target

The development of antimalarial drugs remains a public health priority, and the orotidine 5′-monophosphate decarboxylase from Plasmodium falciparum (PfOMPDC) has great potential as a drug target. The crystallization of PfOMPDC with substrate bound represents an important advance for structure-based drug-design efforts [Tokuoka et al. (2008), J. Biochem. 143, 69–78]. The complex of the enzyme bound to the substrate OMP (PDB entry 2za1) would be of particular utility in this regard. However, re-refinement of this structure of the Michaelis complex shows that the bound ligand is the product rather than the substrate. Here, the re-refinement of a set of three structures, the apo enzyme and two versions of the product-bound form (PDB entries 2za1, 2za2 and 2za3), is reported. The improved geometry and fit of these structures to the observed electron density will enhance their utility in antimalarial drug design.

by Brandt, G.S. at September 21, 2018 12:00 AM

X-ray structure of Arthrobacter globiformis M30 ketose 3-epimerase for the production of d-allulose from d-fructose

The X-ray structure of ketose 3-epimerase from Arthrobacter globiformis M30, which was previously reported to be a d-allulose 3-epimerase (AgD-AE), was determined at 1.96 Å resolution. The crystal belonged to the hexagonal space group P6522, with unit-cell parameters a = b = 103.98, c = 256.53 Å. The structure was solved by molecular replacement using the structure of Mesorhizobium loti l-ribulose 3-epimerase (MlL-RE), which has 41% sequence identity, as a search model. A hexagonal crystal contained two molecules in the asymmetric unit, and AgD-AE formed a homotetramer with twofold symmetry. The overall structure of AgD-AE was more similar to that of MlL-RE than to the known structures of d-psicose (alternative name d-allulose) 3-epimerases (d-PEs or d-AEs), although AgD-AE and MlL-RE have different substrate specificities. Both AgD-AE and MlL-RE have long helices in the C-terminal region that would contribute to the stability of the homotetramer. AgD-AE showed higher enzymatic activity for l-ribulose than d-allulose; however, AgD-AE is stable and is a unique useful enzyme for the production of d-allulose from d-fructose.

by Kamitori, S. at September 21, 2018 12:00 AM

Redox manipulation of the manganese metal in human manganese superoxide dismutase for neutron diffraction

Human manganese superoxide dismutase (MnSOD) is one of the most significant enzymes in preventing mitochondrial dysfunction and related diseases by combating reactive oxygen species (ROS) in the mitochondrial matrix. Mitochondria are the source of up to 90% of cellular ROS generation, and MnSOD performs its necessary bioprotective role by converting superoxide into oxygen and hydrogen peroxide. This vital catalytic function is conducted via cyclic redox reactions between the substrate and the active-site manganese using proton-coupled electron transfers. Owing to protons being difficult to detect experimentally, the series of proton transfers that compose the catalytic mechanism of MnSOD are unknown. Here, methods are described to discern the proton-based mechanism using chemical treatments to control the redox state of large perdeuterated MnSOD crystals and subsequent neutron diffraction. These methods could be applicable to other crystal systems in which proton information on the molecule in question in specific chemical states is desired.

by Borgstahl, G.E.O. at September 21, 2018 12:00 AM

Cryo-neutron crystallographic data collection and preliminary refinement of left-handed Z-DNA d(CGCGCG)

Crystals of left-handed Z-DNA [d(CGCGCG)]2 diffract X-rays to beyond 1 Å resolution, feature a small unit cell (∼18 × 31 × 44 Å) and are well hydrated, with around 90 water molecules surrounding the duplex in the asymmetric unit. The duplex shows regular hydration patterns in the narrow minor groove, on the convex surface and around sugar–phosphate backbones. Therefore, Z-DNA offers an ideal case to test the benefits of low-temperature neutron diffraction data collection to potentially determine the donor–acceptor patterns of first- and second-shell water molecules. Nucleic acid fragments pose challenges for neutron crystallography because water molecules are located on the surface rather than inside sequestered spaces such as protein active sites or channels. Water molecules can be expected to display dynamic behavior, particularly in cases where water is not part of an inner shell and directly coordinated to DNA atoms. Thus, nuclear density maps based on room-temperature diffraction data with a resolution of 1.6 Å did not allow an unequivocal determination of the orientations of water molecules. Here, cryo-neutron diffraction data collection for a Z-DNA crystal on the Macromolecular Neutron Diffractometer at the Spallation Neutron Source at Oak Ridge National Laboratory and the outcome of an initial refinement of the structure are reported. A total of 12 diffraction images were recorded with an exposure time of 3.5 h per image, whereby the crystal was static for each diffraction image with a 10° φ rotation between images. Initial refinements using these neutron data indicated the positions and orientations of 30 water molecules within the first hydration shell of the DNA molecule. This experiment constitutes a state-of-the-art approach and is the first attempt to our knowledge to determine the low-temperature neutron structure of a DNA crystal.

by Egli, M. at September 21, 2018 12:00 AM

Nature

Discovery of Galileo’s long-lost letter shows he edited his heretical ideas to fool the Inquisition

Discovery of Galileo’s long-lost letter shows he edited his heretical ideas to fool the Inquisition

Discovery of Galileo’s long-lost letter shows he edited his heretical ideas to fool the Inquisition, Published online: 21 September 2018; doi:10.1038/d41586-018-06769-4

Exclusive: Document shows that the astronomer toned down the claims that triggered science history’s most infamous battle — then lied about his edits.

by Alison Abbott at September 21, 2018 12:00 AM

Discovery of vibrant deep-sea life prompts new worries over seabed mining

Discovery of vibrant deep-sea life prompts new worries over seabed mining

Discovery of vibrant deep-sea life prompts new worries over seabed mining, Published online: 21 September 2018; doi:10.1038/d41586-018-06771-w

“Gummy squirrels,” single-celled organisms the size of softballs and strange worms thrive in a Pacific Ocean zone some considered an underwater desert.

by Amy Maxmen at September 21, 2018 12:00 AM

University says prominent food researcher committed academic misconduct

University says prominent food researcher committed academic misconduct

University says prominent food researcher committed academic misconduct, Published online: 21 September 2018; doi:10.1038/d41586-018-06802-6

Brian Wansink will retire at the end of the academic year, according to Cornell University.

by Sara Reardon at September 21, 2018 12:00 AM

Japan’s asteroid mission drops first rovers onto ‘dumpling’ space rock

Japan’s asteroid mission drops first rovers onto ‘dumpling’ space rock

Japan’s asteroid mission drops first rovers onto ‘dumpling’ space rock, Published online: 21 September 2018; doi:10.1038/d41586-018-06808-0

The two landers will hop around Ryugu to take pictures and measure temperatures.

by Elizabeth Gibney at September 21, 2018 12:00 AM

Daily briefing: The cruel and futile war on obesity

Daily briefing: The cruel and futile war on obesity

Daily briefing: The cruel and futile war on obesity, Published online: 21 September 2018; doi:10.1038/d41586-018-06810-6

The human cost of science’s inability to understand obesity, Galileo’s long-lost heretical letter, and our pick of the best images, features and culture from the week in science.

by Flora Graham at September 21, 2018 12:00 AM