Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age
Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the f...
Source: Acta Crystallographica Section F - December 24, 2018 Category: Biochemistry Authors: Mitra, A.K. Tags: cryo-EM single-particle analysis three-dimensional reconstruction phase plates direct detectors topical reviews Source Type: research
Acta Crystallographica Section F – another home for cryo-electron microscopy contributions
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - December 24, 2018 Category: Biochemistry Authors: Mitra, A.K. van Raaij, M. Tags: cryo-EM introduction editorial Source Type: research
AtNPR4 from Arabidopsis thaliana: expression, purification, crystallization and crystallographic analysis
In this study, Spodoptera frugiperda (Sf9) cells were used to express full-length AtNPR4 from Arabidopsis thaliana. To facilitate crystallization, T4 lysozyme (T4L) was added to the N-terminus of the AtNPR4 protein. The recombinant T4L-AtNPR4 protein was expressed, purified and crystallized using the sitting-drop and hanging-drop vapour-diffusion methods. The T4L-AtNPR4 crystals have symmetry consistent with space group C2, with unit-cell parameters a = 93.7, b = 85.8, c = 88.2 Å , β = 90 ° and one molecule per asymmetric unit. The best crystal diffracted to a resolution of 2.75 Å . Structure d...
Source: Acta Crystallographica Section F - December 22, 2018 Category: Biochemistry Authors: Yang, Q. Zhang, M. Zheng, J. Jia, Z. Tags: salicylic acid systemic acquired resistance protein purification regulatory mechanism crystal diffraction Arabidopsis thaliana research communications Source Type: research
The redefined DNA-binding domain of human xeroderma pigmentosum complementation group A: production, crystallization and structure solution
Human xeroderma pigmentosum complementation group A (XPA) is a scaffold protein that plays significant roles in DNA-damage verification and in recruiting downstream endonucleases to facilitate the repair of DNA lesions in nucleotide-excision repair. XPA98 – 219 (residues 98 – 219) has been identified as a DNA-binding domain and has been extensively studied in the last two decades. However, the most recent studies have redefined the DNA-binding domain as XPA98 – 239 (residues 98 – 239); it exerts a remarkably higher DNA-binding affinity than XPA98 – 219 and has a binding affinity that is quite ...
Source: Acta Crystallographica Section F - December 22, 2018 Category: Biochemistry Authors: Lian, F.-M. Yang, X. Yang, W. Jiang, Y.-L. Qian, C. Tags: XPA DNA-binding domain nucleotide-excision repair research communications Source Type: research
The structure and activity of the glutathione reductase from Streptococcus pneumoniae
The glutathione reductase (GR) from Streptococcus pneumoniae is a flavoenzyme that catalyzes the reduction of oxidized glutathione (GSSG) to its reduced form (GSH) in the cytoplasm of this bacterium. The maintenance of an intracellular pool of GSH is critical for the detoxification of reactive oxygen and nitrogen species and for intracellular metal tolerance to ions such as zinc. Here, S. pneumoniae GR (SpGR) was overexpressed and purified and its crystal structure determined at 2.56 Å resolution. SpGR shows overall structural similarity to other characterized GRs, with a dimeric structure that includes an antipa...
Source: Acta Crystallographica Section F - December 22, 2018 Category: Biochemistry Authors: Sikanyika, M. Arag ã o, D. McDevitt, C.A. Maher, M.J. Tags: glutathione reductase X-ray crystallography Streptococcus pneumoniae research communications Source Type: research
The X-ray crystal structure of human endothelin 1, a polypeptide hormone regulator of blood pressure
Human endothelin is a 21-amino-acid polypeptide, constrained by two intra-chain disulfide bridges, that is made by endothelial cells. It is the most potent vasoconstrictor in the body and is crucially important in the regulation of blood pressure. It plays a major role in a host of medical conditions, including hypertension, diabetes, stroke and cancer. Endothelin was crystallized 28 years ago in the putative space group P6122, but the structure was never successfully solved by X-ray diffraction. Using X-ray diffraction data from 1992, the structure has now been solved. Assuming a unit cell belonging to space group P61 and...
Source: Acta Crystallographica Section F - December 22, 2018 Category: Biochemistry Authors: McPherson, A. Larson, S.B. Tags: endothelin blood pressure vasoconstrictors polypeptide hormones twinned crystals crystallographic archeology research communications Source Type: research
Never too late for endothelin
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - December 22, 2018 Category: Biochemistry Authors: Stanfield, R.L. Tags: endothelin archiving raw data scientific commentaries Source Type: research
Single-particle reconstruction statistics: a diagnostic tool in solving biomolecular structures by cryo-EM
This study revisits the theory of 3D reconstruction and demonstrates how the associated statistics can provide a diagnostic tool to improve SPA. Small numbers of images already give sufficient information on micrograph quality and the amount of data required to reach high resolution. Such feedback allows the microscopist to improve sample-preparation and imaging parameters before committing to extensive data collection. Once a larger data set is available, a B factor can be determined describing the suppression of the signal owing to one or more causes, such as specimen movement, radiation damage, alignment inaccuracy and ...
Source: Acta Crystallographica Section F - December 22, 2018 Category: Biochemistry Authors: Heymann, J.B. Tags: cryo-EM cryo-electron microscopy spectral signal-to-noise ratio single-particle analysis Fourier shell correlation image processing research communications Source Type: research
Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy
Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - December 22, 2018 Category: Biochemistry Authors: Sorzano, C.O.S. Jim é nez, A. Mota, J. Vilas, J.L. Maluenda, D. Mart í nez, M. Ram í rez-Aportela, E. Majtner, T. Segura, J. S á nchez-Garc í a, R. Rancel, Y. del Ca ñ o, L. Conesa, P. Melero, R. Jonic, S. Vargas, J. Cazals, F. Freyberg, Z. Krieger, Tags: electron microscopy image processing continuous heterogeneity single-particle analysis normal-mode analysis research communications Source Type: research
On cross-correlations, averages and noise in electron microscopy
Biological samples are radiation-sensitive and require imaging under low-dose conditions to minimize damage. As a result, images contain a high level of noise and exhibit signal-to-noise ratios that are typically significantly smaller than 1. Averaging techniques, either implicit or explicit, are used to overcome the limitations imposed by the high level of noise. Averaging of 2D images showing the same molecule in the same orientation results in highly significant projections. A high-resolution structure can be obtained by combining the information from many single-particle images to determine a 3D structure. Similarly, a...
Source: Acta Crystallographica Section F - December 21, 2018 Category: Biochemistry Authors: Radermacher, M. Ruiz, T. Tags: image processing signal-to-noise ratio cross-correlation multireference alignment 3D reference-based projection alignment research communications Source Type: research
The structure of SDS22 provides insights into the mechanism of heterodimer formation with PP1
Protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. The vast majority of regulators are intrinsically disordered proteins (IDPs) and bind PP1 via short linear motifs within their intrinsically disordered regions. One of the most ancient PP1 regulators is SDS22, a protein that is conserved from yeast to mammals. Sequence analysis of SDS22 revealed that it is a leucine-rich repeat (LRR) protein, suggesting that SDS22, unlike nearly every other known PP1 regulator, is not an IDP but instead is fully structured. ...
Source: Acta Crystallographica Section F - November 30, 2018 Category: Biochemistry Authors: Choy, M.S. Bolik-Coulon, N. Archuleta, T.L. Peti, W. Page, R. Tags: SDS22 protein phosphatase 1 LRR protein PP1 regulator research communications Source Type: research
Crystal structure of the Agrobacterium tumefaciens type VI effector – immunity complex
The type VI secretion system (T6SS) comprises needle-shaped multisubunit complexes that play a role in the microbial defense systems of Gram-negative bacteria. Some Gram-negative bacteria harboring a T6SS deliver toxic effector proteins into the cytoplasm or periplasm of competing bacteria in order to lyse and kill them. To avoid self-cell disruption, these bacteria have cognate immunity proteins that inhibit their toxic effector proteins. T6SS amidase effector protein 4 (Tae4) and T6SS amidase immunity protein 4 (Tai4) are a representative of the toxic effector – immunity pairs of the T6SS. Here, the three-dimension...
Source: Acta Crystallographica Section F - November 30, 2018 Category: Biochemistry Authors: Fukuhara, S. Nakane, T. Yamashita, K. Ishii, R. Ishitani, R. Nureki, O. Tags: Agrobacterium tumefaciens type VI effector – immunity complex crystal structure Tae4 Tai4 research communications Source Type: research
The crystal structure of Mycobacterium tuberculosis high-temperature requirement A protein reveals an autoregulatory mechanism
The crystal structure of Mycobacterium tuberculosis high-temperature requirement A (HtrA) protein was determined at 1.83 Å resolution. This membrane-associated protease is essential for the survival of M. tuberculosis. The crystal structure reveals that interactions between the PDZ domain and the catalytic domain in HtrA lead to an inactive conformation. This finding is consistent with its proposed role as a regulatory protease that is conditionally activated upon appropriate environmental triggers. The structure provides a basis for directed studies to evaluate the role of this essential protein and the regulato...
Source: Acta Crystallographica Section F - November 29, 2018 Category: Biochemistry Authors: Gupta, A.K. Behera, D. Gopal, B. Tags: regulated proteolysis high-temperature requirement A protein PDZ domain Mycobacterium tuberculosis research communications Source Type: research
An inexpensive system for imaging the contents of multi-well plates
An inexpensive system for automated imaging of the contents of 12-, 24- and 96-well plates has been built. The xyz stage is constructed from parts from a light-duty computer numerical control wood-carving/engraving machine, and the Arduino-based board was wired so that it can trigger still images or movies though a microscope-mounted digital camera. The translation stage provides reproducible three-dimensional movement of the sample over a volume of 160 mm in x, 100 mm in y and 40 mm in z. A Python script generates the G-code command file that scans the plate and collects a series of z-stacked images of each sa...
Source: Acta Crystallographica Section F - November 29, 2018 Category: Biochemistry Authors: Bohm, A. Tags: automated microscope imaging system multi-well plates research communications Source Type: research
Structural studies of a glycoside hydrolase family 3 β -glucosidase from the model fungus Neurospora crassa
The glycoside hydrolase family 3 (GH3) β -glucosidases are a structurally diverse family of enzymes. Cel3A from Neurospora crassa (NcCel3A) belongs to a subfamily of key enzymes that are crucial for industrial biomass degradation. β -Glucosidases hydrolyse the β -1,4 bond at the nonreducing end of cellodextrins. The hydrolysis of cellobiose is of special importance as its accumulation inhibits other cellulases acting on crystalline cellulose. Here, the crystal structure of the biologically relevant dimeric form of NcCel3A is reported. The structure has been refined to 2.25 Å resolution, with an Rcr...
Source: Acta Crystallographica Section F - November 26, 2018 Category: Biochemistry Authors: Karkehabadi, S. Hansson, H. Mikkelsen, N.E. Kim, S. Kaper, T. Sandgren, M. Gudmundsson, M. Tags: glycoside hydrolase family 3 β -glucosidase biodegradation crystal structure Neurospora crassa NcCel3A research communications Source Type: research
Crystal structure of the dimethylsulfide monooxygenase DmoA from Hyphomicrobium sulfonivorans
DmoA is a monooxygenase which uses dioxygen (O2) and reduced flavin mononucleotide (FMNH2) to catalyze the oxidation of dimethylsulfide (DMS). Although it has been characterized, the structure of DmoA remains unknown. Here, the crystal structure of DmoA was determined to a resolution of 2.28 Å and was compared with those of its homologues LadA and BdsA. The results showed that their overall structures are similar: they all share a conserved TIM-barrel fold which is composed of eight α -helices and eight β -strands. In addition, they all have five additional insertions. Detailed comparison showed that t...
Source: Acta Crystallographica Section F - November 26, 2018 Category: Biochemistry Authors: Cao, H.-Y. Wang, P. Peng, M. Shao, X. Chen, X.-L. Li, C.-Y. Tags: dimethylsulfide monooxygenase sulfur cycle TIM-barrel fold substrate-binding pocket Hyphomicrobium sulfonivorans research communications Source Type: research
Structures of endo-1,5- α -l-arabinanase mutants from Bacillus thermodenitrificans TS-3 in complex with arabino-oligosaccharides
In this study, the crystal structures of inactive ABN-TS mutants, D27A and D147N, were determined in complex with arabino-oligosaccharides. The crystal structures revealed that ABN-TS has at least six subsites in the deep V-shaped cleft formed across one face of the propeller structure. The structural features indicate that substrate recognition is profoundly influenced by the remote subsites as well as by the subsites surrounding the active center. The `open' structure of the substrate-binding cleft of the endo-acting ABN-TS is suitable for the random binding of several sugar units in polymeric substrates. (Source: Acta C...
Source: Acta Crystallographica Section F - November 26, 2018 Category: Biochemistry Authors: Yamaguchi, A. Sogabe, Y. Fukuoka, S. Sakai, T. Tada, T. Tags: arabinanases endo-acting enzymes biofuels Bacillus thermodenitrificans endo-1,5- α -l-arabinanase mutants crystal structure – substrate complex glycoside hydrolase family 43 research communications Source Type: research
Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways
Lactobacillus brevis alcohol dehydrogenase (LbADH) is a well studied homotetrameric enzyme which catalyzes the enantioselective reduction of prochiral ketones to the corresponding secondary alcohols. LbADH is stable and enzymatically active at elevated temperatures and accepts a broad range of substrates, making it a valuable tool in industrial biocatalysis. Here, the expression, purification and crystallization of LbADH to generate large, single crystals with a volume of up to 1 mm3 suitable for neutron diffraction studies are described. Neutron diffraction data were collected from an H/D-exchanged LbADH crystal using...
Source: Acta Crystallographica Section F - November 26, 2018 Category: Biochemistry Authors: Hermann, J. Nowotny, P. Schrader, T.E. Biggel, P. Hekmat, D. Weuster-Botz, D. Tags: short-chain dehydrogenases/reductases protein crystallization neutron diffraction hydrogen-bonding network Lactobacillus brevis alcohol dehydrogenase research communications Source Type: research
X-ray crystallographic analysis of the catalytic domain of α -1,3-glucanase FH1 from Paenibacillus glycanilyticus overexpressed in Brevibacillus choshinensis
In this study, the recombinant catalytic domain of α -1,3-glucanase FH1 from Paenibacillus glycanilyticus FH11, which is classified into glycoside hydrolase family 87, was prepared using a Brevibacillus choshinensis expression system and purified in a soluble form. Crystals of the purified protein were produced by the sitting-drop vapor-diffusion method. Diffraction data were collected to a resolution of 1.6 Å using synchrotron radiation. The crystals obtained belonged to the tetragonal space group P41212 or P43212, with unit-cell parameters a = b = 132.6, c = 76.1 Å . ...
Source: Acta Crystallographica Section F - November 16, 2018 Category: Biochemistry Authors: Intuy, R. Itoh, T. Suyotha, W. Hayashi, J. Yano, S. Makabe, K. Wakayama, M. Hibi, T. Tags: α -1,3-glucanase catalytic domains Paenibacillus glycanilyticus research communications Source Type: research
Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii
Undecaprenyl pyrophosphate (UPP) is an important carrier of the oligosaccharide component in peptidoglycan synthesis. Inhibition of UPP synthase (UPPS) may be an effective strategy in combating the pathogen Acinetobacter baumannii, which has evolved to be multidrug-resistant. Here, A. baumannii UPPS (AbUPPS) was cloned, expressed, purified and crystallized, and its structure was determined by X-ray diffraction. Each chain of the dimeric protein folds into a central β -sheet with several surrounding α -helices, including one at the C-terminus. In the active site, two molecules of citrate interact with the side ch...
Source: Acta Crystallographica Section F - November 16, 2018 Category: Biochemistry Authors: Ko, T.-P. Huang, C.-H. Lai, S.-J. Chen, Y. Tags: undecaprenyl pyrophosphate synthase Acinetobacter baumannii peptidoglycan research communications Source Type: research
Combining crystallogenesis methods to produce diffraction-quality crystals of a psychrophilic tRNA-maturation enzyme
The determination of conditions for the reproducible growth of well diffracting crystals is a critical step in every biocrystallographic study. On the occasion of a new structural biology project, several advanced crystallogenesis approaches were tested in order to increase the success rate of crystallization. These methods included screening by microseed matrix screening, optimization by counter-diffusion and crystal detection by trace fluorescent labeling, and are easily accessible to any laboratory. Their combination proved to be particularly efficient in the case of the target, a 48 kDa CCA-adding enzyme from the p...
Source: Acta Crystallographica Section F - October 31, 2018 Category: Biochemistry Authors: de Wijn, R. Hennig, O. Ernst, F.G.M. Lorber, B. Betat, H. M ö rl, M. Sauter, C. Tags: microseeding counter-diffusion trace fluorescent labeling optimization crystallogenesis tRNA maturation CCA-adding enzyme Planococcus halocryophilus research communications Source Type: research
Crystal structure of glycosyltrehalose synthase from Sulfolobus shibatae DSM5389
Glycosyltrehalose synthase (GTSase) converts the glucosidic bond between the last two glucose residues of amylose from an α -1,4 bond to an α -1,1 bond, generating a nonreducing glycosyl trehaloside, in the first step of the biosynthesis of trehalose. To better understand the structural basis of the catalytic mechanism, the crystal structure of GTSase from the hyperthermophilic archaeon Sulfolobus shibatae DSM5389 (5389-GTSase) has been determined to 2.4 Å resolution by X-ray crystallography. The structure of 5389-GTSase can be divided into five domains. The central domain contains the ( β / &alp...
Source: Acta Crystallographica Section F - October 31, 2018 Category: Biochemistry Authors: Okazaki, N. Blaber, M. Kuroki, R. Tamada, T. Tags: trehalose glycosyltransferase GH13 family glycosyltrehalose synthase Sulfolobus shibatae research communications Source Type: research
Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum
(S)-3-Hydroxybutyryl-CoA dehydrogenase (HBD) has been gaining increased attention recently as it is a key enzyme in the enantiomeric formation of (S)-3-hydroxybutyryl-CoA [(S)-3HB-CoA]. It converts acetoacetyl-CoA to (S)-3HB-CoA in the synthetic metabolic pathway. (S)-3HB-CoA is further modified to form (S)-3-hydroxybutyrate, which is a source of biodegradable polymers. During the course of a study to develop biodegradable polymers, attempts were made to determine the crystal structure of HBD from Clostridium acetobutylicum (CacHBD), and the crystal structures of both apo and NAD+-bound forms of CacHBD were determined. The...
Source: Acta Crystallographica Section F - October 31, 2018 Category: Biochemistry Authors: Takenoya, M. Taguchi, S. Yajima, S. Tags: bio-based plastics enzyme kinetics fatty-acid metabolism SDR superfamily X-ray protein crystallography research communications Source Type: research
Quo vadis, Acta Crystallographica F?
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - October 31, 2018 Category: Biochemistry Authors: van Raaij, M.J. Tags: editorial Acta Crystallographica F publishing scientific society journals Source Type: research
Crystal structures and kinetics of N-acetylneuraminate lyase from Fusobacterium nucleatum
In this study, atomic resolution structures of NanA from Fusobacterium nucleatum (FnNanA) in ligand-free and ligand-bound forms are reported at 2.32 and 1.76 Å resolution, respectively. F. nucleatum is a Gram-negative pathogen that causes gingival and periodontal diseases in human hosts. Like other bacterial N-acetylneuraminate lyases, FnNanA also shares the triosephosphate isomerase (TIM)-barrel fold. As observed in other homologous enzymes, FnNanA forms a tetramer. In order to characterize the structure – function relationship, the steady-state kinetic parameters of the enzyme are also reported. (Source: ...
Source: Acta Crystallographica Section F - October 17, 2018 Category: Biochemistry Authors: Kumar, J.P. Rao, H. Nayak, V. Ramaswamy, S. Tags: N-acetylneuraminate lyase sialic acid catabolism enzyme kinetics Fusobacterium nucleatum research communications Source Type: research
High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form
Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various inhibitors have been reported. Many of these crystals belong to the same crystal form and most of the reported structures have resolutions in the range 3.2 – 2.3 Å . Here, three new crystal forms of human IDO1 obtained by introducing a surface mutation, K116A/K117A, distant from the active site are reported. One of these crystal forms diffracted to 1.5 Å...
Source: Acta Crystallographica Section F - October 17, 2018 Category: Biochemistry Authors: Luo, S. Xu, K. Xiang, S. Chen, J. Chen, C. Guo, C. Tong, Y. Tong, L. Tags: indoleamine 2,3-dioxygenase 1 cancer immunotherapy heme proteins tryptophan metabolism crystal engineering research communications Source Type: research
BpeB, a major resistance-nodulation-cell division transporter from Burkholderia cenocepacia: construct design, crystallization and preliminary structural analysis
Burkholderia cenocepacia is an opportunistic pathogen that infects cystic fibrosis patients, causing pneumonia and septicemia. B. cenocepacia has intrinsic antibiotic resistance against monobactams, aminoglycosides, chloramphenicol and fluoroquinolones that is contributed by a homologue of BpeB, which is a member of the resistance-nodulation-cell division (RND)-type multidrug-efflux transporters. Here, the cloning, overexpression, purification, construct design for crystallization and preliminary X-ray diffraction analysis of this BpeB homologue from B. cenocepacia are reported. Two truncation variants were designed to rem...
Source: Acta Crystallographica Section F - October 16, 2018 Category: Biochemistry Authors: Horikawa, T. Hung, L.-W. Kim, H.-B. Shaya, D. Kim, C.-Y. Terwilliger, T.C. Yamashita, E. Aoki, M. Okada, U. Murakami, S. Tags: membrane transporter multidrug resistance drug exporter Burkholderia research communications Source Type: research
Crystal structures of the N-terminal domain of the Staphylococcus aureus DEAD-box RNA helicase CshA and its complex with AMP
In this study, the crystal structures of the N-terminal RecA-like domain 1 of S. aureus CshA (SaCshAR1) and of its complex with AMP (SaCshAR1 – AMP) are reported at resolutions of 1.5 and 1.8 Å , respectively. SaCshAR1 adopts a conserved α / β RecA-like structure with seven parallel strands surrounded by nine α -helices. The Q motif and motif I are responsible for the binding of the adenine group and phosphate group of AMP, respectively. Structure comparison of SaCshAR1 – AMP and SaCshAR1 reveals that motif I undergoes a conformational change upon AMP binding. Isothermal titration cal...
Source: Acta Crystallographica Section F - October 16, 2018 Category: Biochemistry Authors: Chen, X. Wang, C. Zhang, X. Tian, T. Zang, J. Tags: CshA DEAD-box RNA helicase Staphylococcus aureus AMP crystallography research communications Source Type: research
Crystallization of ectonucleotide phosphodiesterase/pyrophosphatase-3 and orientation of the SMB domains in the full-length ectodomain
Ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3, ENPP3) is an ATP-hydrolyzing glycoprotein that is located in the extracellular space. The full-length ectodomain of rat NPP3 was expressed in HEK293S GntI − cells, purified using two chromatographic steps and crystallized. Its structure at 2.77 Å resolution reveals that the active-site zinc ions are missing and a large part of the active site and the surrounding residues are flexible. The SMB-like domains have the same orientation in all four molecules in the asymmetric unit. The SMB2 domain is oriented as in NPP2, but the SMB1 domain does not intera...
Source: Acta Crystallographica Section F - October 16, 2018 Category: Biochemistry Authors: D ö hler, C. Zebisch, M. Krinke, D. Robitzki, A. Str ä ter, N. Tags: ectonucleotide phosphodiesterase/pyrophosphatase NPP3 ectonucleotidase ATP hydrolysis allergic response research communications Source Type: research
Characterization and structure determination of a llama-derived nanobody targeting the J-base binding protein 1
J-base binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J ( β -d-glucosylhydroxymethyluracil), a modification of thymidine confined to some protozoa. Camelid (llama) single-domain antibody fragments (nanobodies) targeting JBP1 were produced for use as crystallization chaperones. Surface plasmon resonance screening identified Nb6 as a strong binder, recognizing JBP1 with a 1:1 stoichiometry and high affinity (Kd = 30 nM). Crystallization trials of JBP1 in complex with Nb6 yielded crystals that diffracted to 1.47 Å resolution. However, the dimensions of the asymmetric unit a...
Source: Acta Crystallographica Section F - October 16, 2018 Category: Biochemistry Authors: van Beusekom, B. Heidebrecht, T. Adamopoulos, A. Fish, A. Pardon, E. Steyaert, J. Joosten, R.P. Perrakis, A. Tags: nanobodies J-base binding protein 1 llamas immune system research communications Source Type: research
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. Nu...
Source: Acta Crystallographica Section F - September 21, 2018 Category: Biochemistry Authors: Harp, J.M. Coates, L. Sullivan, B. Egli, M. Tags: neutron diffraction cryogenic data collection oligonucleotide hydration Z-DNA research communications Source Type: research
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...
Source: Acta Crystallographica Section F - September 21, 2018 Category: Biochemistry Authors: Azadmanesh, J. Lutz, W.E. Weiss, K.L. Coates, L. Borgstahl, G.E.O. Tags: manganese superoxide dismutase neutron diffraction perdeuteration human oxidation reduction large unit cell research communications Source Type: research
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 overal...
Source: Acta Crystallographica Section F - September 21, 2018 Category: Biochemistry Authors: Yoshida, H. Yoshihara, A. Gullapalli, P.K. Ohtani, K. Akimitsu, K. Izumori, K. Kamitori, S. Tags: Arthrobacter globiformis ketose 3-epimerase β / α -barrel d-allulose X-ray structure research communications Source Type: research
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 sub...
Source: Acta Crystallographica Section F - September 21, 2018 Category: Biochemistry Authors: Novak, W.R.P. West, K.H.J. Kirkman, L.M.D. Brandt, G.S. Tags: orotidine 5 ′ -monophosphate decarboxylase Plasmodium falciparum Michaelis complex re-refinement research communications Source Type: research
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 ...
Source: Acta Crystallographica Section F - September 21, 2018 Category: Biochemistry Authors: Sharma, R. Gangwar, S.P. Saxena, A.K. Tags: prostate cancer ETS transcription factor ERG3 E74 promoter DNA X-ray structure comparative structure analysis research communications Source Type: research
Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-l-phenylalanine
The X-ray crystal structures of two superfolder green fluorescent protein (sfGFP) constructs containing a genetically incorporated spectroscopic reporter unnatural amino acid, 4-nitro-l-phenylalanine (pNO2F), at two unique sites in the protein have been determined. Amber codon-suppression methodology was used to site-specifically incorporate pNO2F at a solvent-accessible (Asp133) and a partially buried (Asn149) site in sfGFP. The Asp133pNO2F sfGFP construct crystallized with two molecules per asymmetric unit in space group P3221 and the crystal structure was refined to 2.05 Å resolution. Crystals of Asn149pNO2F s...
Source: Acta Crystallographica Section F - September 19, 2018 Category: Biochemistry Authors: Maurici, N. Savidge, N. Lee, B.U. Brewer, S.H. Phillips-Piro, C.M. Tags: 4-nitro-l-phenylalanine unnatural amino acids noncanonical amino acids green fluorescent protein research communications Source Type: research
The novel metallo- β -lactamase PNGM-1 from a deep-sea sediment metagenome: crystallization and X-ray crystallographic analysis
In this study, PNGM-1 was overexpressed, purified and crystallized. Crystals of native and selenomethionine-substituted PNGM-1 diffracted to 2.10 and 2.30 Å resolution, respectively. Both the native and the selenomethionine-labelled PNGM-1 crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 122, b = 83, c = 163 Å , β = 110 ° . Matthews coefficient (VM) calculations suggested the presence of 6 – 10 molecules in the asymmetric unit, corresponding to a solvent content of ∼ 31 – 58%. Structure determination is currently in progress. (Source: Acta Cryst...
Source: Acta Crystallographica Section F - September 19, 2018 Category: Biochemistry Authors: Park, K.S. Hong, M.-K. Jeon, J.W. Kim, J.H. Jeon, J.H. Lee, J.H. Kim, T.Y. Karim, A.M. Malik, S.K. Kang, L.-W. Lee, S.H. Tags: deep-sea sediment Edison Seamount metagenome antibiotic resistance metallo- β -lactamase research communications Source Type: research
Crystal structure of mutant carboxypeptidase T from Thermoactinomyces vulgaris with an implanted S1 ′ subsite from pancreatic carboxypeptidase B
A site-directed mutagenesis method has been used to obtain the G215S/A251G/T257A/D260G/T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris (CPT), in which the amino-acid residues of the S1 ′ subsite are substituted by the corresponding residues from pancreatic carboxypeptidase B (CPB). It was shown that the mutant enzyme retained the broad, mainly hydrophobic selectivity of wild-type CPT. The mutant containing the implanted CPB S1 ′ subsite was crystallized and its three-dimensional structure was determined at 1.29 Å resolution by X-ray crystallography. A comparison of the three-dimensi...
Source: Acta Crystallographica Section F - September 19, 2018 Category: Biochemistry Authors: Akparov, V.K. Timofeev, V.I. Kuranova, I.P. Rakitina, T.V. Tags: metallocarboxypeptidase T Thermoactinomyces vulgaris metallocarboxypeptidase B S1 ′ subsite substrate selectivity X-ray crystallography research communications Source Type: research
Crystal structure of the ribonuclease-P-protein subunit from Staphylococcus aureus
Staphylococcus aureus ribonuclease-P-protein subunit (RnpA) is a promising antimicrobial target that is a key protein component for two essential cellular processes, RNA degradation and transfer-RNA (tRNA) maturation. The first crystal structure of RnpA from the pathogenic bacterial species, S. aureus, is reported at 2.0 Å resolution. The structure presented maintains key similarities with previously reported RnpA structures from bacteria and archaea, including the highly conserved RNR-box region and aromatic residues in the precursor-tRNA 5 ′ -leader-binding domain. This structure will be instrumental in t...
Source: Acta Crystallographica Section F - September 19, 2018 Category: Biochemistry Authors: Ha, L. Colquhoun, J. Noinaj, N. Das, C. Dunman, P.M. Flaherty, D.P. Tags: ribonucleoprotein structure RnpA RNase P protein Staphylococcus aureus tRNA research communications Source Type: research
Crystal structure of Arabidopsis thaliana peroxiredoxin A C119S mutant
This article reports the crystal structure of a PrxA C119S mutant refined to 2.6 Å resolution. The protein exists as a decamer both in the crystal structure and in solution. The structure is in the reduced state suitable for the approach of peroxide, though conformational changes are needed for the resolving process. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 19, 2018 Category: Biochemistry Authors: Yang, Y. Cai, W. Wang, J. Pan, W. Liu, L. Wang, M. Zhang, M. Tags: peroxiredoxins peroxiredoxin A Arabidopsis thaliana redox regulation chloroplast thioredoxin systems oxidative and photo-oxidative stress research communications Source Type: research
Structure of glyoxysomal malate dehydrogenase (MDH3) from Saccharomyces cerevisiae
Malate dehydrogenase (MDH), a carbohydrate and energy metabolism enzyme in eukaryotes, catalyzes the interconversion of malate to oxaloacetate (OAA) in conjunction with that of nicotinamide adenine dinucleotide (NAD+) to NADH. Three isozymes of MDH have been reported in Saccharomyces cerevisiae: MDH1, MDH2 and MDH3. MDH1 is a mitochondrial enzyme and a member of the tricarboxylic acid cycle, whereas MDH2 is a cytosolic enzyme that functions in the glyoxylate cycle. MDH3 is a glyoxysomal enzyme that is involved in the reoxidation of NADH, which is produced during fatty-acid β -oxidation. The affinity of MDH3 for OAA is...
Source: Acta Crystallographica Section F - September 19, 2018 Category: Biochemistry Authors: Moriyama, S. Nishio, K. Mizushima, T. Tags: malate dehydrogenase glyoxysome fatty-acid β -oxidation X-ray crystallography MDH3 Saccharomyces cerevisiae research communications Source Type: research
Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase
Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 18.104.22.168) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD+, and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD+-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves ...
Source: Acta Crystallographica Section F - September 19, 2018 Category: Biochemistry Authors: Gonz á lez, J.M. Marti-Arbona, R. Chen, J.C.-H. Broom-Peltz, B. Unkefer, C.J. Tags: malate dehydrogenase methylotrophs biofuels Methylobacterium extorquens research communications Source Type: research
Investigation into the binding of dyes within protein crystals
It was found that the crystals of at least a dozen different proteins could be thoroughly stained to an intense color with a panel of dyes. Many, if not most, of the stained protein crystals retained the dyes almost indefinitely when placed in large volumes of dye-free mother liquor. Dialysis experiments showed that most of the dyes that were retained in crystals also bound to the protein when free in solution; less frequently, some dyes bound only in the crystal. The experiments indicated a strong association of the dyes with the proteins. Four protein crystals were investigated by X-ray diffraction to ascertain the mode ...
Source: Acta Crystallographica Section F - September 3, 2018 Category: Biochemistry Authors: McPherson, A. Larson, S.B. Tags: dyes stains disordered binding detergents difference Fourier complexes colored crystals staining protein crystals research communications Source Type: research
X-ray structure of alisporivir in complex with cyclophilin A at 1.5 Å resolution
This study provides detailed molecular insights into the CypA – ALV interaction. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 3, 2018 Category: Biochemistry Authors: Dujardin, M. Bouckaert, J. Rucktooa, P. Hanoulle, X. Tags: cyclophilins peptidylprolyl isomerase alisporivir inhibitors isomerases non-immunosuppressive CsA derivative HIV HCV Duchenne muscular dystrophy research communications Source Type: research
TssA from Aeromonas hydrophila: expression, purification and crystallographic studies
TssA is a core subunit of the type VI secretion system, which is a major player in interspecies competition in Gram-negative bacteria. Previous studies on enteroaggregative Escherichia coli TssA suggested that it is comprised of three putative domains: a conserved N-terminal domain, a middle domain and a ring-forming C-terminal domain. X-ray studies of the latter two domains have identified their respective structures. Here, the results of the expression and purification of full-length and domain constructs of TssA from Aeromonas hydrophila are reported, resulting in diffraction-quality crystals for the middle domain (Nt2)...
Source: Acta Crystallographica Section F - September 3, 2018 Category: Biochemistry Authors: Dix, S.R. Sun, R. Harris, M.J. Batters, S.L. Sedelnikova, S.E. Baker, P.J. Thomas, M.S. Rice, D.W. Tags: type VI secretion system TssA subunit Aeromonas hydrophila research communications Source Type: research
Mosquito-larvicidal binary toxin receptor protein (Cqm1): crystallization and X-ray crystallographic analysis
Cqm1 from Culex quinquefasciatus has been identified as the receptor for Lysinibacillus sphaericus binary toxin (BinAB). It is an amylomaltase that is presented on the epithelial membrane in the larval midgut through a glycosyl-phosphatidylinositol anchor. The active core of this protein (residues 23 – 560) was overexpressed in Escherichia coli, purified and successfully crystallized by the sitting-drop vapor-diffusion method using d-arabinose and CaCl2 as additives, as identified using high-throughput differential scanning fluorimetry analysis. X-ray diffraction data were collected to a resolution of 2.8 Å...
Source: Acta Crystallographica Section F - September 3, 2018 Category: Biochemistry Authors: Sharma, M. Lakshmi, A. Gupta, G.D. Kumar, V. Tags: Cqm1 Culex quinquefasciatus binary toxin receptor protein Lysinibacillus sphaericus amylomaltase mosquito-larvicidal binary toxin crystallization research communications Source Type: research
Staphylococcus aureus lipase: purification, kinetic characterization, crystallization and crystallographic study
Staphylococcus aureus lipase (SAL), a triacylglycerol esterase, is an important virulence factor in S. aureus and may be a therapeutic target for infectious diseases caused by S. aureus. For the purposes of anti-SAL drug development using structure-based drug design, X-ray crystallographic analysis of SAL overexpressed in Escherichia coli was performed. The recombinant protein was purified using a three-step protocol involving immobilized metal-affinity chromatography, cation-exchange chromatography and anion-exchange chromatography flowthrough methods, yielding 40 mg of protein per litre of bacterial culture. Crystals...
Source: Acta Crystallographica Section F - September 3, 2018 Category: Biochemistry Authors: Tanaka, M. Kamitani, S. Kitadokoro, K. Tags: lipase Staphylococcus aureus virulence factors toxins crystallization research communications Source Type: research
Serendipitous crystallization and structure determination of bacterioferritin from Achromobacter
Bacterioferritins (Bfrs) are ferritin-like molecules with a hollow spherical 24-mer complex design that are unique to bacterial and archaeal species. They play a critical role in storing iron(III) within the complex at concentrations much higher than the feasible solubility limits of iron(III), thus maintaining iron homeostasis within cells. Here, the crystal structure of bacterioferritin from Achromobacter (Ach Bfr) that crystallized serendipitously during a crystallization attempt of an unrelated mycobacterial protein is reported at 1.95 Å resolution. Notably, Fe atoms were bound to the structure along with a p...
Source: Acta Crystallographica Section F - August 29, 2018 Category: Biochemistry Authors: Dwivedy, A. Jha, B. Singh, K.H. Ahmad, M. Ashraf, A. Kumar, D. Biswal, B.K. Tags: bacterioferritin Achromobacter dinuclear center iron storage heme research communications Source Type: research
MBP-binding DARPins facilitate the crystallization of an MBP fusion protein
The production of high-quality crystals is the main bottleneck in determining the structures of proteins using X-ray crystallography. In addition to being recognized as a very effective solubility-enhancing fusion partner, Escherichia coli maltose-binding protein (MBP) has also been successfully employed as a `fixed-arm' crystallization chaperone in more than 100 cases. Here, it is reported that designed ankyrin-repeat proteins (DARPins) that bind with high affinity to MBP can promote the crystallization of an MBP fusion protein when the fusion protein alone fails to produce diffraction-quality crystals. As a proof of prin...
Source: Acta Crystallographica Section F - August 29, 2018 Category: Biochemistry Authors: Gumpena, R. Lountos, G.T. Waugh, D.S. Tags: crystallization chaperones designed ankyrin-repeat proteins dual-specificity phosphatase 1 maltose-binding protein surface-entropy-reduction mutagenesis research communications Source Type: research
MSMEG_6292, a Mycobacterium smegmatis RNA polymerase secondary channel-binding protein: purification, crystallization and X-ray diffraction analysis
The transcriptional activity of RNA polymerase (RNAP) is controlled by a diverse set of regulatory factors. A subset of these regulators modulate the activity of RNAP through its secondary channel. Gre factors reactivate stalled elongation complexes by enhancing the intrinsic cleavage activity of RNAP. In the present study, the protein MSMEG_6292, a Gre-factor homologue from Mycobacterium smegmatis, was expressed heterologously in Escherichia coli and purified using standard chromatographic techniques. The hanging-drop vapour-diffusion crystallization method yielded diffraction-quality crystals. The crystals belonged to th...
Source: Acta Crystallographica Section F - August 29, 2018 Category: Biochemistry Authors: Joseph, A. Nagaraja, V. Natesh, R. Tags: transcription regulation RNA polymerase Gre-factor homologue mycobacteria X-ray diffraction Mycobacterium smegmatis MSMEG_6292 research communications Source Type: research