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Acta Crystallographica. Section D, Biological Crystallography

Beatriz Herguedas, Isaias Lans, María Sebastián, Juan A Hermoso, Marta Martínez-Júlvez, Milagros Medina
Riboflavin kinases (RFKs) catalyse the phosphorylation of riboflavin to produce FMN. In most bacteria this activity is catalysed by the C-terminal module of a bifunctional enzyme, FAD synthetase (FADS), which also catalyses the transformation of FMN into FAD through its N-terminal FMN adenylyltransferase (FMNAT) module. The RFK module of FADS is a homologue of eukaryotic monofunctional RFKs, while the FMNAT module lacks homologyto eukaryotic enzymes involved in FAD production. Previously, the crystal structure of Corynebacterium ammoniagenes FADS (CaFADS) was determined in its apo form...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Takanori Nakane, Changyong Song, Mamoru Suzuki, Eriko Nango, Jun Kobayashi, Tetsuya Masuda, Shigeyuki Inoue, Eiichi Mizohata, Toru Nakatsu, Tomoyuki Tanaka, Rie Tanaka, Tatsuro Shimamura, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Makina Yabashi, Osamu Nureki, So Iwata, Michihiro Sugahara
Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Tao Zhang, Deqiang Yao, Jiawei Wang, Yuanxin Gu, Haifu Fan
A post-experimental identification/purification procedure similar to that described in Zhang et al. [(2015), IUCrJ, 2, 322-326] has been proposed for use in the treatment of multiphase protein serial crystallography (SX) diffraction snapshots. As a proof of concept, the procedure was tested using theoretical serial femtosecond crystallography (SFX) data from a mixture containing native and derivatized crystals of a protein. Two known proteins were taken as examples. Multiphase diffraction snapshots were subjected to two rounds of indexing using the program CrystFEL [White et al...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Magdalena Schacherl, Angelika A M Montada, Elena Brunstein, Ulrich Baumann
The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins from Helicobacter and Salmonella. The first crystal structure analysis of a U32 catalytic domain from Methanopyrus kandleri (gene mk0906) reveals a modified (βα)8 TIM-barrel fold with some unique features...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Jiří Dostál, Adam Pecina, Olga Hrušková-Heidingsfeldová, Lucie Marečková, Iva Pichová, Pavlina Řezáčová, Martin Lepšík, Jiří Brynda
The virulence of the Candida pathogens is enhanced by the production of secreted aspartic proteases, which therefore represent possible targets for drug design. Here, the crystal structure of the secreted aspartic protease Sapp2p from Candida parapsilosis was determined. Sapp2p was isolated from its natural source and crystallized in complex with pepstatin A, a classical aspartic protease inhibitor. The atomic resolution of 0.83 Å allowed the protonation states of the active-site residues to be inferred...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Neelanjana Janardan, Rajesh K Harijan, Tiila Riikka Kiema, Rikkert K Wierenga, M R N Murthy
Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) from Mycobacterium smegmatis in apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domain via flexible hinge regions, generating an asymmetric tetramer...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Maithili Saoji, Paul J Paukstelis
DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson-Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Yunfei Wu, Chengliang Wang, Shenglong Lin, Minhao Wu, Lu Han, Changlin Tian, Xuan Zhang, Jianye Zang
Staphylococcus aureus is a Gram-positive bacterium with strong pathogenicity that causes a wide range of infections and diseases. Enolase is an evolutionarily conserved enzyme that plays a key role in energy production through glycolysis. Additionally, enolase is located on the surface of S. aureus and is involved in processes leading to infection. Here, crystal structures of Sa_enolase with and without bound phosphoenolpyruvate (PEP) are presented at 1.6 and 2.45 Å resolution, respectively. The structure reveals an octameric arrangement; however, both dimeric and octameric conformations were observed in solution...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Marta Ferraroni, Sonia Del Prete, Daniela Vullo, Clemente Capasso, Claudiu T Supuran
Carbonic anhydrase (CA) is a zinc enzyme that catalyzes the reversible conversion of carbon dioxide to bicarbonate (hydrogen carbonate) and a proton. CAs have been extensively investigated owing to their involvement in numerous physiological and pathological processes. Currently, CA inhibitors are widely used as antiglaucoma, anticancer and anti-obesity drugs and for the treatment of neurological disorders. Recently, the potential use of CA inhibitors to fight infections caused by protozoa, fungi and bacteria has emerged as a new research direction...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Hodaya V Solomon, Orly Tabachnikov, Shifra Lansky, Rachel Salama, Hadar Feinberg, Yuval Shoham, Gil Shoham
Geobacillus stearothermophilus T-6 is a Gram-positive thermophilic soil bacterium that contains a battery of degrading enzymes for the utilization of plant cell-wall polysaccharides, including xylan, arabinan and galactan. A 9.4 kb gene cluster has recently been characterized in G. stearothermophilus that encodes a number of galactan-utilization elements. A key enzyme of this degradation system is Gan42B, an intracellular GH42 β-galactosidase capable of hydrolyzing short β-1,4-galactosaccharides into galactose units, making it of high potential for various biotechnological applications...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Tomasz Manszewski, Kriti Singh, Barbara Imiolczyk, Mariusz Jaskolski
S-Adenosyl-L-homocysteine hydrolase (SAHase) is involved in the enzymatic regulation of S-adenosyl-L-methionine (SAM)-dependent methylation reactions. After methyl-group transfer from SAM, S-adenosyl-L-homocysteine (SAH) is formed as a byproduct, which in turn is hydrolyzed to adenosine (Ado) and homocysteine (Hcy) by SAHase. The crystal structure of BeSAHase, an SAHase from Bradyrhizobium elkanii, which is a nitrogen-fixing bacterial symbiont of legume plants, was determined at 1.7 Å resolution, showing the domain organization (substrate-binding domain, NAD(+) cofactor-binding domain and dimerization domain) of the subunits...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Nicholas Skar-Gislinge, Søren A R Kynde, Ilia G Denisov, Xin Ye, Ivan Lenov, Stephen G Sligar, Lise Arleth
Membrane proteins reconstituted into phospholipid nanodiscs comprise a soluble entity accessible to solution small-angle X-ray scattering (SAXS) studies. It is demonstrated that using SAXS data it is possible to determine both the shape and localization of the membrane protein cytochrome P450 3A4 (CYP3A4) while it is embedded in the phospholipid bilayer of a nanodisc. In order to accomplish this, a hybrid approach to analysis of small-angle scattering data was developed which combines an analytical approach to describe the multi-contrast nanodisc with a free-form bead-model description of the embedded protein...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Hugo Serrano-Posada, Sara Centeno-Leija, Sonia Patricia Rojas-Trejo, Claudia Rodríguez-Almazán, Vivian Stojanoff, Enrique Rudiño-Piñera
During X-ray data collection from a multicopper oxidase (MCO) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the X-ray-induced reduction of O2 to 2H2O at the trinuclear copper cluster (TNC) of the enzyme. In this work, 12 crystallographic structures of Thermus thermophilus HB27 multicopper oxidase (Tth-MCO) in holo, apo and Hg-bound forms and with different X-ray absorbed doses have been determined. In holo Tth-MCO structures with four Cu atoms, the proton-donor residue Glu451 involved in O2 reduction was found in a double conformation: Glu451a (∼7 Å from the TNC) and Glu451b (∼4...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Roisin M McMahon, Mathieu Coinçon, Stephanie Tay, Begoña Heras, Craig J Morton, Martin J Scanlon, Jennifer L Martin
Pseudomonas aeruginosa is an opportunistic human pathogen for which new antimicrobial drug options are urgently sought. P. aeruginosa disulfide-bond protein A1 (PaDsbA1) plays a pivotal role in catalyzing the oxidative folding of multiple virulence proteins and as such holds great promise as a drug target. As part of a fragment-based lead discovery approach to PaDsbA1 inhibitor development, the identification of a crystal form of PaDsbA1 that was more suitable for fragment-soaking experiments was sought. A previously identified crystallization condition for this protein was unsuitable, as in this crystal form of PaDsbA1 the active-site surface loops are engaged in the crystal packing, occluding access to the target site...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Alessandra Del Giudice, Nicolae Viorel Pavel, Luciano Galantini, Giuseppe Falini, Paolo Trost, Simona Fermani, Francesca Sparla
Oxygenic photosynthetic organisms produce sugars through the Calvin-Benson cycle, a metabolism that is tightly linked to the light reactions of photosynthesis and is regulated by different mechanisms, including the formation of protein complexes. Two enzymes of the cycle, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), form a supramolecular complex with the regulatory protein CP12 with the formula (GAPDH-CP122-PRK)2, in which both enzyme activities are transiently inhibited during the night...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Keren Green, Nasrin Qasim, Garik Gdaelvsky, Anna Kogan, Yehuda Goldgur, Abraham H Parola, Ofra Lotan, Orna Almog
Tryptophanase (Trpase) is a pyridoxal 5'-phosphate (PLP)-dependent homotetrameric enzyme which catalyzes the degradation of L-tryptophan. Trpase is also known for its cold lability, which is a reversible loss of activity at low temperature (2°C) that is associated with the dissociation of the tetramer. Escherichia coli Trpase dissociates into dimers, while Proteus vulgaris Trpase dissociates into monomers. As such, this enzyme is an appropriate model to study the protein-protein interactions and quaternary structure of proteins...
December 1, 2015: Acta Crystallographica. Section D, Biological Crystallography
Vaheh Oganesyan, Yariv Mazor, Chunning Yang, Kimberly E Cook, Robert M Woods, Andrew Ferguson, Michael A Bowen, Tom Martin, Jie Zhu, Herren Wu, William F Dall'Acqua
The three-dimensional structure of a human IgG1 Fc fragment bound to wild-type human FcγRI is reported. The structure of the corresponding complex was solved at a resolution of 2.4 Å using molecular replacement; this is the highest resolution achieved for an unmutated FcγRI molecule. This study highlights the critical structural and functional role played by the second extracellular subdomain of FcγRI. It also explains the long-known major energetic contribution of the Fc `LLGG' motif at positions 234-237, and particularly of Leu235, via a `lock-and-key' mechanism...
November 2015: Acta Crystallographica. Section D, Biological Crystallography
Michail N Isupov, Ewald Schröder, Robert P Gibson, Jean Beecher, Giuliana Donadio, Vahid Saneei, Stephlina A Dcunha, Emma J McGhie, Christopher Sayer, Colin F Davenport, Peter C Lau, Yoshie Hasegawa, Hiroaki Iwaki, Maria Kadow, Kathleen Balke, Uwe T Bornscheuer, Gleb Bourenkov, Jennifer A Littlechild
The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer-Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model. The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily...
November 2015: Acta Crystallographica. Section D, Biological Crystallography
Ulrich Zander, Gleb Bourenkov, Alexander N Popov, Daniele de Sanctis, Olof Svensson, Andrew A McCarthy, Ekaterina Round, Valentin Gordeliy, Christoph Mueller-Dieckmann, Gordon A Leonard
Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented...
November 2015: Acta Crystallographica. Section D, Biological Crystallography
Wuan Geok Saw, Giancarlo Tria, Ardina Grüber, Malathy Sony Subramanian Manimekalai, Yongqian Zhao, Arun Chandramohan, Ganesh Srinivasan Anand, Tsutomu Matsui, Thomas M Weiss, Subhash G Vasudevan, Gerhard Grüber
Infection by the four serotypes of Dengue virus (DENV-1 to DENV-4) causes an important arthropod-borne viral disease in humans. The multifunctional DENV nonstructural protein 5 (NS5) is essential for capping and replication of the viral RNA and harbours a methyltransferase (MTase) domain and an RNA-dependent RNA polymerase (RdRp) domain. In this study, insights into the overall structure and flexibility of the entire NS5 of all four Dengue virus serotypes in solution are presented for the first time. The solution models derived revealed an arrangement of the full-length NS5 (NS5FL) proteins with the MTase domain positioned at the top of the RdRP domain...
November 2015: Acta Crystallographica. Section D, Biological Crystallography
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