The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution
In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to &...
Source: Acta Crystallographica Section F - November 25, 2016 Category: Biochemistry Authors: Cala, A.R. Nadeau, M.T. Abendroth, J. Staker, B.L. Reers, A.R. Weatherhead, A.W. Dobson, R.C.J. Myler, P.J. Hudson, A.O. Tags: Bartonella henselae dihydrodipicolinate reductase diaminopimelate lysine biosynthesis cat-scratch disease research communications Source Type: research
Coxsackievirus B3 protease 3C: expression, purification, crystallization and preliminary structural insights
Viral proteases are proteolytic enzymes that orchestrate the assembly of viral components during the viral life cycle and proliferation. Here, the expression, purification, crystallization and preliminary X-ray diffraction analysis are presented of protease 3C, the main protease of an emerging enterovirus, coxsackievirus B3, that is responsible for many cases of viral myocarditis. Polycrystalline protein precipitates suitable for X-ray powder diffraction (XRPD) measurements were produced in the presence of 22 – 28%(w/v) PEG 4000, 0.1 M Tris – HCl, 0.2 M MgCl2 in a pH range from 7.0 to 8.5. A polymorph o...
Source: Acta Crystallographica Section F - November 25, 2016 Category: Biochemistry Authors: Fili, S. Valmas, A. Christopoulou, M. Spiliopoulou, M. Nikolopoulos, N. Lichi è re, J. Logotheti, S. Karavassili, F. Rosmaraki, E. Fitch, A. Wright, J. Beckers, D. Degen, T. Nenert, G. Hilgenfeld, R. Papageorgiou, N. Canard, B. Coutard, B. Margiolaki, I. Tags: 3C protease coxsackievirus B3 powder diffraction research communications Source Type: research
The crystal structure of the endoglucanase Cel10, a family 8 glycosyl hydrolase from Klebsiella pneumoniae
Cellulases are produced by microorganisms that grow on cellulose biomass. Here, a cellulase, Cel10, was identified in a strain of Klebsiella pneumoniae isolated from Chinese bamboo rat gut. Analysis of substrate specificity showed that Cel10 is able to hydrolyze amorphous carboxymethyl cellulose (CMC) and crystalline forms of cellulose (Avicel and xylan) but is unable to hydrolyze p-nitrophenol β -d-glucopyranoside (p-NPG), proving that Cel10 is an endoglucanase. A phylogenetic tree analysis indicates that Cel10 belongs to the glycoside hydrolase 8 (GH8) subfamily. In order to further understanding of its substrate sp...
Source: Acta Crystallographica Section F - November 25, 2016 Category: Biochemistry Authors: Attigani, A. Sun, L. Wang, Q. Liu, Y. Bai, D. Li, S. Huang, X. Tags: cellulases Klebsiella pneumoniae carboxymethyl cellulase cellulose biosynthesis crystal structure Cel10 research communications Source Type: research
Crystal structure of the toxin Msmeg_6760, the structural homolog of Mycobacterium tuberculosis Rv2035, a novel type II toxin involved in the hypoxic response
The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin – antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate – latch mechanism. The function of the Msmeg_6760 toxin is unknown, but structure-based predictions revealed th...
Source: Acta Crystallographica Section F - November 18, 2016 Category: Biochemistry Authors: Bajaj, R.A. Arbing, M.A. Shin, A. Cascio, D. Miallau, L. Tags: Mycobacterium smegmatis Mycobacterium tuberculosis X-ray crystallography protein structure toxin – antitoxin complexes bacterial latency macrophage infection novel folds research communications Source Type: research
1.45 Å resolution structure of SRPN18 from the malaria vector Anopheles gambiae
Serine protease inhibitors (serpins) in insects function within development, wound healing and immunity. The genome of the African malaria vector, Anopheles gambiae, encodes 23 distinct serpin proteins, several of which are implicated in disease-relevant physiological responses. A. gambiae serpin 18 (SRPN18) was previously categorized as non-inhibitory based on the sequence of its reactive-center loop (RCL), a region responsible for targeting and initiating protease inhibition. The crystal structure of A. gambiae SRPN18 was determined to a resolution of 1.45 Å , including nearly the entire RCL in one of the two m...
Source: Acta Crystallographica Section F - November 18, 2016 Category: Biochemistry Authors: Meekins, D.A. Zhang, X. Battaile, K.P. Lovell, S. Michel, K. Tags: serpins serine proteases insect immunity enzyme inhibitors mosquito Anopheles gambiae malaria vector research communications Source Type: research
Structural characterization of the thermostable Bradyrhizobium japonicumd-sorbitol dehydrogenase
Bradyrhizobium japonicum sorbitol dehydrogenase is NADH-dependent and is active at elevated temperatures. The best substrate is d-glucitol (a synonym for d-sorbitol), although l-glucitol is also accepted, giving it particular potential in industrial applications. Crystallization led to a hexagonal crystal form, with crystals diffracting to 2.9 Å resolution. In attempts to phase the data, a molecular-replacement solution based upon PDB entry 4nbu (33% identical in sequence to the target) was found. The solution contained one molecule in the asymmetric unit, but a tetramer similar to that found in other short-chain...
Source: Acta Crystallographica Section F - October 27, 2016 Category: Biochemistry Authors: Fredslund, F. Otten, H. Gemperlein, S. Poulsen, J.-C.N. Carius, Y. Kohring, G.-W. Lo Leggio, L. Tags: sorbitol dehydrogenase thermostability glucitol research communications Source Type: research
Development of a high-throughput crystal structure-determination platform for JAK1 using a novel metal-chelator soaking system
Crystals of phosphorylated JAK1 kinase domain were initially generated in complex with nucleotide (ADP) and magnesium. The tightly bound Mg2+-ADP at the ATP-binding site proved recalcitrant to ligand displacement. Addition of a molar excess of EDTA helped to dislodge the divalent metal ion, promoting the release of ADP and allowing facile exchange with ATP-competitive small-molecule ligands. Many kinases require the presence of a stabilizing ligand in the ATP site for crystallization. This procedure could be useful for developing co-crystallization systems with an exchangeable ligand to enable structure-based drug design o...
Source: Acta Crystallographica Section F - October 27, 2016 Category: Biochemistry Authors: Caspers, N.L. Han, S. Rajamohan, F. Hoth, L.R. Geoghegan, K.F. Subashi, T.A. Vazquez, M.L. Kaila, N. Cronin, C.N. Johnson, E. Kurumbail, R.G. Tags: Janus kinase kinases crystal soaking ligand exchange structure-based drug design research communications Source Type: research
Crystal structure of fuculose aldolase from the Antarctic psychrophilic yeast Glaciozyma antarctica PI12
In this study, the gene encoding FucA from Glaciozyma antarctica PI12 (GaFucA) was cloned and the enzyme was overexpressed in Escherichia coli, purified and crystallized. The tetrameric structure of GaFucA was determined to 1.34 Å resolution. The overall architecture of GaFucA and its catalytically essential histidine triad are highly conserved among other fuculose aldolases. Comparisons of structural features between GaFucA and its mesophilic and thermophilic homologues revealed that the enzyme has typical psychrophilic attributes, indicated by the presence of a high number of nonpolar residues at the surface an...
Source: Acta Crystallographica Section F - October 27, 2016 Category: Biochemistry Authors: Jaafar, N.R. Littler, D. Beddoe, T. Rossjohn, J. Illias, R.M. Mahadi, N.M. Mackeen, M.M. Murad, A.M.A. Abu Bakar, F.D. Tags: psychrophiles crystallization metalloenzymes fuculose aldolase l-fuculose metabolism Glaciozyma antarctica imino cyclitols research communications Source Type: research
Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope – Fab complexes
Herein, multiple crystal structures of meditope peptide derivatives incorporating natural and unnatural amino acids bound to the cetuximab Fab domain are presented. The affinity of each derivative was determined by surface plasmon resonance and correlated to the atomic structure. Overall, it was observed that the hydrophobic residues in the meditope peptide, Phe3, Leu5 and Leu10, could accommodate a number of moderate substitutions, but these invariably reduced the overall affinity and half-life of the interaction. In one case, the substitution of Phe3 by histidine led to a change in the rotamer conformation, in which the ...
Source: Acta Crystallographica Section F - October 24, 2016 Category: Biochemistry Authors: Bzymek, K.P. Avery, K.A. Ma, Y. Horne, D.A. Williams, J.C. Tags: meditope monoclonal antibody cetuximab unnatural amino acids X-ray crystallography surface plasmon resonance research communications Source Type: research
The structure of the metallo- β -lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor
In this study, three triazolylthioacetamides were tested as inhibitors of VIM-2. One of the tested compounds showed clear inhibition of VIM-2, with an IC50 of 20 µ M. The crystal structure of the inhibitor in complex with VIM-2 was obtained by DMSO-free co-crystallization and was solved at a resolution of 1.50 Å . To our knowledge, this is the first structure of a triazolylthioacetamide inhibitor in complex with an MBL. Analysis of the structure shows that the inhibitor binds to the two zinc ions in the active site of VIM-2 and revealed detailed information on the interactions involved. Furthermore, the...
Source: Acta Crystallographica Section F - October 24, 2016 Category: Biochemistry Authors: Christopeit, T. Yang, K.-W. Yang, S.-K. Leiros, H.-K.S. Tags: antibiotic resistance DMSO-free co-crystallization carbapenemases VIM-2 metallo- β -lactamases research communications Source Type: research
Crystal structure of a phosphoribosyl anthranilate isomerase from the hyperthermophilic archaeon Thermococcus kodakaraensis
A phosphoribosyl anthranilate isomerase, TkTrpF, from Thermococcus kodakaraensis was expressed in Escherichia coli and purified to homogeneity. TkTrpF was crystallized and its structure was determined by molecular replacement in two different space groups (C2 and P1) using data to 1.85 and 1.75 Å resolution, respectively. TkTrpF belongs to the class of TIM-barrel proteins. Structural comparison with other phosphoribosyl anthranilate isomerases (TrpFs) showed the highest structural similarity to Pyrococcus furiosus TrpF. Similarly to P. furiosus TrpF, TkTrpF is a monomer in solution, in contrast to other thermophi...
Source: Acta Crystallographica Section F - October 24, 2016 Category: Biochemistry Authors: Perveen, S. Rashid, N. Papageorgiou, A.C. Tags: tryptophan biosynthesis protein stability TIM barrel hyperthermophilic archaea Pyrococcus furiosus Thermococcus kodakaraensis phosphoribosyl anthranilate isomerase research communications Source Type: research
Crystal structures of a yeast 14-3-3 protein from Lachancea thermotolerans in the unliganded form and bound to a human lipid kinase PI4KB-derived peptide reveal high evolutionary conservation
14-3-3 proteins bind phosphorylated binding partners to regulate several of their properties, including enzymatic activity, stability and subcellular localization. Here, two crystal structures are presented: the crystal structures of the 14-3-3 protein (also known as Bmh1) from the yeast Lachancea thermotolerans in the unliganded form and bound to a phosphopeptide derived from human PI4KB (phosphatidylinositol 4-kinase B). The structures demonstrate the high evolutionary conservation of ligand recognition by 14-3-3 proteins. The structural analysis suggests that ligand recognition by 14-3-3 proteins evolved very early in t...
Source: Acta Crystallographica Section F - October 24, 2016 Category: Biochemistry Authors: Eisenreichova, A. Klima, M. Boura, E. Tags: 14-3-3 proteins Bmh1 Bmh2 crystal structure phosphopeptide PI4KB Lachancea thermotolerans research communications Source Type: research
Expression and crystallographic studies of the Arabidopsis thaliana GDP-d-mannose pyrophosphorylase VTC1
GDP-d-mannose pyrophosphorylase catalyzes the production of GDP-d-mannose, an intermediate product in the plant ascorbic acid (AsA) biosynthetic pathway. This enzyme is a key regulatory target in AsA biosynthesis and is encoded by VITAMIN C DEFECTIVE 1 (VTC1) in the Arabidopsis thaliana genome. Here, recombinant VTC1 was expressed, purified and crystallized. Diffraction data were obtained from VTC1 crystals grown in the absence and presence of substrate using X-rays. The ligand-free VTC1 crystal diffracted X-rays to 3.3 Å resolution and belonged to space group R32, with unit-cell parameters a = b = 183.6, c = 368...
Source: Acta Crystallographica Section F - September 27, 2016 Category: Biochemistry Authors: Zhao, S. Liu, L. Tags: ascorbic acid biosynthesis GDP-d-mannose pyrophosphorylase Arabidopsis thaliana research communications Source Type: research
Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography
Multicopper oxidases oxidize various phenolic and nonphenolic compounds by using molecular oxygen as an electron acceptor to produce water. A multicopper oxidase protein, CueO, from Escherichia coli is involved in copper homeostasis in the bacterial cell. Although X-ray crystallographic studies have been conducted, the reduction mechanism of oxygen and the proton-transfer pathway remain unclear owing to the difficulty in identifying H atoms from X-ray diffraction data alone. To elucidate the reaction mechanism using neutron crystallography, a preparation system for obtaining large, high-quality single crystals of deuterate...
Source: Acta Crystallographica Section F - September 22, 2016 Category: Biochemistry Authors: Akter, M. Inoue, C. Komori, H. Matsuda, N. Sakurai, T. Kataoka, K. Higuchi, Y. Shibata, N. Tags: multicopper oxidase CueO deuteration X-ray diffraction neutron diffraction research communications Source Type: research
X-ray crystallographic studies of the extracellular domain of the first plant ATP receptor, DORN1, and the orthologous protein from Camelina sativa
Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses in Arabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein, Camelina sativa lectin receptor kinase I.9 (csLecRK-I.9-ECD or csI.9-ECD). A variety of deglycosylation strategies were employed to optimize t...
Source: Acta Crystallographica Section F - September 22, 2016 Category: Biochemistry Authors: Li, Z. Chakraborty, S. Xu, G. Tags: plant ATP receptor DORN1 lectin receptor kinase I.9 glycosylation Arabidopsis thaliana Camelina sativa research communications Source Type: research
Crystallographic study of the 2-thioribothymidine-synthetic complex TtuA – TtuB from Thermus thermophilus
In this study, the TtuA – TtuB complex from Thermus thermophilus was expressed, purified and crystallized. To mimic the thiocarboxylated TtuB, the C-terminal Gly residue was replaced with Cys (G65C) to obtain crystals of the TtuA – TtuB complex. A Zn-MAD data set was collected to a resolution of 2.5 Å . MAD analysis successfully determined eight Zn sites, and a partial structure model composed of four TtuA – TtuB complexes in the asymmetric unit was constructed. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 22, 2016 Category: Biochemistry Authors: Chen, M. Narai, S. Omura, N. Shigi, N. Chimnaronk, S. Tanaka, Y. Yao, M. Tags: post-transcriptional modification sulfur transfer ubiquitin-like protein Zn-MAD TtuA TtuB research communications Source Type: research
Crystal structure of rofecoxib bound to human cyclooxygenase-2
Rofecoxib (Vioxx) was one of the first selective cyclooxygenase-2 (COX-2) inhibitors (coxibs) to be approved for use in humans. Within five years after its release to the public, Vioxx was withdrawn from the market owing to the adverse cardiovascular effects of the drug. Despite the widespread knowledge of the development and withdrawal of Vioxx, relatively little is known at the molecular level about how the inhibitor binds to COX-2. Vioxx is unique in that the inhibitor contains a methyl sulfone moiety in place of the sulfonamide moiety found in other coxibs such as celecoxib and valdecoxib. Here, new crystallization con...
Source: Acta Crystallographica Section F - September 22, 2016 Category: Biochemistry Authors: Orlando, B.J. Malkowski, M.G. Tags: cyclooxygenase rofecoxib nonsteroidal anti-inflammatory drugs Vioxx crystal structure research communications Source Type: research
Comparative analysis of anti-polyglutamine Fab crystals grown on Earth and in microgravity
Huntington's disease is one of nine neurodegenerative diseases caused by a polyglutamine (polyQ)-repeat expansion. An anti-polyQ antigen-binding fragment, MW1 Fab, was crystallized both on Earth and on the International Space Station, a microgravity environment where convection is limited. Once the crystals returned to Earth, the number, size and morphology of all crystals were recorded, and X-ray data were collected from representative crystals. The results generally agreed with previous microgravity crystallization studies. On average, microgravity-grown crystals were 20% larger than control crystals grown on Earth, and ...
Source: Acta Crystallographica Section F - September 22, 2016 Category: Biochemistry Authors: Owens, G.E. New, D.M. Olvera, A.I. Manzella, J.A. Macon, B.L. Dunn, J.C. Cooper, D.A. Rouleau, R.L. Connor, D.S. Bjorkman, P.J. Tags: Huntington's disease International Space Station microgravity polyglutamine X-ray crystallography huntingtin crystallization research communications Source Type: research
The structure of a glycoside hydrolase 29 family member from a rumen bacterium reveals unique, dual carbohydrate-binding domains
Glycoside hydrolase (GH) family 29 consists solely of α -l-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29_0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes. The microbial species that provided the source of this enzyme is unknown. This enzyme contains a second carbohydrate-binding domain at its C-terminal end in addition to the typical N-terminal catalytic domain and carbohydrate-binding domain arrangement of GH29-family prot...
Source: Acta Crystallographica Section F - September 22, 2016 Category: Biochemistry Authors: Summers, E.L. Moon, C.D. Atua, R. Arcus, V.L. Tags: GH29 glycoside hydrolase α -l-fucosidase carbohydrate-binding domain CBM32 PDB5K9H research communications Source Type: research
Crystal and solution structural studies of mouse phospholipid hydroperoxide glutathione peroxidase 4
The mammalian glutathione peroxidase (GPx) family is a key component of the cellular antioxidative defence system. Within this family, GPx4 has unique features as it accepts a large class of hydroperoxy lipid substrates and has a plethora of biological functions, including sperm maturation, regulation of apoptosis and cerebral embryogenesis. In this paper, the structure of the cytoplasmic isoform of mouse phospholipid hydroperoxide glutathione peroxidase (O70325-2 GPx4) with selenocysteine 46 mutated to cysteine is reported solved at 1.8 Å resolution using X-ray crystallography. Furthermore, solution data of an i...
Source: Acta Crystallographica Section F - September 22, 2016 Category: Biochemistry Authors: Janowski, R. Scanu, S. Niessing, D. Madl, T. Tags: phospholipid hydroperoxide glutathione peroxidase 4 reactive oxidative species NMR spectroscopy small-angle X-ray scattering research communications Source Type: research
Arabidopsis receptor-like cytoplasmic kinase BIK1: purification, crystallization and X-ray diffraction analysis
In this study, the purification and crystallization of a first member of the class VI family of RLCK proteins, BIK1, are reported. BIK1 was crystallized using the microbatch-under-oil method. X-ray diffraction data were collected to 2.35 Å resolution. The crystals belonged to the monoclinic space group C2, with two monomers per asymmetric unit. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 22, 2016 Category: Biochemistry Authors: Lal, N.K. Fisher, A.J. Dinesh-Kumar, S.P. Tags: receptor-like kinase receptor-like cytoplasmic kinases RLCK BIK1 BOTRYTIS-INDUCED KINASE 1 PAMP-triggered immunity Arabidopsis research communications Source Type: research
Crystal structure of yeast monothiol glutaredoxin Grx6 in complex with a glutathione-coordinated [2Fe – 2S] cluster
Glutaredoxins (Grxs) constitute a superfamily of proteins that perform diverse biological functions. The Saccharomyces cerevisiae glutaredoxin Grx6 not only serves as a glutathione (GSH)-dependent oxidoreductase and as a GSH transferase, but also as an essential [2Fe – 2S]-binding protein. Here, the dimeric structure of the C-terminal domain of Grx6 (holo Grx6C), bridged by one [2Fe – 2S] cluster coordinated by the active-site Cys136 and two external GSH molecules, is reported. Structural comparison combined with multiple-sequence alignment demonstrated that holo Grx6C is similar to the [2Fe – 2S] cluster...
Source: Acta Crystallographica Section F - September 22, 2016 Category: Biochemistry Authors: Abdalla, M. Dai, Y.-N. Chi, C.-B. Cheng, W. Cao, D.-D. Zhou, K. Ali, W. Chen, Y. Zhou, C.-Z. Tags: glutaredoxin iron – sulfur cluster Saccharomyces cerevisiae crystal structure oxidoreductase research communications Source Type: research
1.65 Å resolution structure of the AraC-family transcriptional activator ToxT from Vibrio cholerae
In this study, a crystal structure of ToxT at 1.65 Å resolution with a similar overall structure to the previously determined structure is reported. However, there are distinct differences between the two structures, particularly in the region that extends from Asp101 to Glu110. This region, which can influence ToxT activity but was disordered in the previous structure, can be traced entirely in the current structure. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 26, 2016 Category: Biochemistry Authors: Li, J. Wehmeyer, G. Lovell, S. Battaile, K.P. Egan, S.M. Tags: AraC ToxT Vibrio cholerae crystal structure palmitoleic acid pathogenesis research communications Source Type: research
Crystal structure of the YajQ-family protein XC_3703 from Xanthomonas campestris pv. campestris
In this study, the structure of XC_3703 was determined to 2.1 Å resolution using the molecular-replacement method. The structure of XC_3703 consists of two domains adopting the same topology, which is similar to that of the RNA-recognition motif (RRM). Arg65, which is conserved among the c-di-GMP-binding subfamily of the YajQ family of proteins, together with Phe80 in domain II, forms a putative c-di-GMP binding site. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 26, 2016 Category: Biochemistry Authors: Zhao, Z. Wu, Z. Zhang, J. Tags: XC_3703 YajQ c-di-GMP receptor research communications Source Type: research
Crystallization of and selenomethionine phasing strategy for a SETMAR – DNA complex
Transposable elements have played a critical role in the creation of new genes in all higher eukaryotes, including humans. Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA-binding domain (DBD) and catalytic domain of the Hsmar1 transposase. The amino-acid sequence of the DBD has been virtually unchanged in 50 million years and, as a consequence, SETMAR retains its sequence-specific binding to the ancestral Hsmar1 terminal inverted repeat (TIR) sequence. Thus, the DNA-binding activity of SETMAR is likely to have an important biological function. To determine the stru...
Source: Acta Crystallographica Section F - August 26, 2016 Category: Biochemistry Authors: Chen, Q. Georgiadis, M. Tags: crystallization DNA-binding domain transposable element terminal inverted repeat Hsmar1 SETMAR research communications Source Type: research
The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase
Interactions of proline-rich motifs with SH3 domains are present in signal transduction and other important cell processes. Analysis of structural and thermodynamic data suggest a relevant role of water molecules in these protein – protein interactions. To determine whether or not the SH3 domain of the Fyn tyrosine kinase shows the same behaviour, the crystal structures of its complexes with two high-affinity synthetic peptides, VSL12 and APP12, which are class I and II peptides, respectively, have been solved. In the class I complexes two water molecules were found at the binding interface that were not present in t...
Source: Acta Crystallographica Section F - August 26, 2016 Category: Biochemistry Authors: Camara-Artigas, A. Ortiz-Salmeron, E. Andujar-S á nchez, M. Bacarizo, J. Martin-Garcia, J.M. Tags: SH3 domain X-ray crystal structure Fyn tyrosine kinase proline-rich motifs research communications Source Type: research
Crystal structure of pyruvate decarboxylase from Zymobacter palmae
Pyruvate decarboxylase (PDC; EC 220.127.116.11) is a thiamine pyrophosphate- and Mg2+ ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15 Å resolution. They belonged to space group P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55 Å and Rr.i.m. = 0.175...
Source: Acta Crystallographica Section F - August 26, 2016 Category: Biochemistry Authors: Buddrus, L. Andrews, E.S.V. Leak, D.J. Danson, M.J. Arcus, V.L. Crennell, S.J. Tags: Zymobacter palmae pyruvate decarboxylase lyase crystal structure TPP-dependent enzyme research communications Source Type: research
Crystal structure of Halobacterium salinarum halorhodopsin with a partially depopulated primary chloride-binding site
In conclusion, the conformation of the chloride-free protein may not be compatible with this crystal form of HsHR despite a packing arrangement that hardly restrains helices E and F that presumably move during ion transport. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 26, 2016 Category: Biochemistry Authors: Schreiner, M. Schlesinger, R. Heberle, J. Niemann, H.H. Tags: halorhodopsin Halobacterium salinarum archaeal rhodopsin retinal protein light-driven ion pump post-crystallization treatment reaction intermediate research communications Source Type: research
Structural analysis of point mutations at the Vaccinia virus A20/D4 interface
This study confirms previous biochemical data and also points out the importance for stability of the restrained conformational space of Pro173. Moreover, these new structures will be useful for the design and rational improvement of known molecules targeting the D4/A20 interface. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - August 9, 2016 Category: Biochemistry Authors: Contesto-Richefeu, C. Tarbouriech, N. Brazzolotto, X. Burmeister, W.P. Peyrefitte, C.N. Iseni, F. Tags: Vaccinia virus DNA replication X-ray structure – π interaction protein protein interface research communications Source Type: research
The quorum-quenching lactonase from Geobacillus caldoxylosilyticus: purification, characterization, crystallization and crystallographic analysis
Lactonases are enzymes that are capable of hydrolyzing various lactones such as aliphatic lactones or acyl-homoserine lactones (AHLs), with the latter being used as chemical signaling molecules by numerous Gram-negative bacteria. Lactonases therefore have the ability to quench the chemical communication, also known as quorum sensing, of numerous bacteria, and in particular to inhibit behaviors that are regulated by this system, such as the expression of virulence factors or the production of biofilms. A novel representative from the metallo- β -lactamase superfamily, dubbed GcL, was isolated from the thermophilic bact...
Source: Acta Crystallographica Section F - August 9, 2016 Category: Biochemistry Authors: Bergonzi, C. Schwab, M. Elias, M. Tags: quorum sensing lactonase thermophile quorum quenching research communications Source Type: research
Crystal structure of Plasmodium falciparum proplasmepsin IV: the plasticity of proplasmepsins
Plasmepsin IV from Plasmodium falciparum (PM IV) is a promising target for the development of novel antimalarial drugs. Here, the crystal structure of the truncated zymogen of PM IV (pPM IV), consisting of the mature enzyme plus a prosegment of 47 residues, has been determined at 1.5 Å resolution. pPM IV presents the fold previously described for studied proplasmepsins, displaying closer similarities to proplasmepin IV from P. vivax (pPvPM) than to the other two proplasmepsins from P. falciparum. The study and comparison of the pPM IV structure with the proplasmepsin structures described previously provide inform...
Source: Acta Crystallographica Section F - August 9, 2016 Category: Biochemistry Authors: Recacha, R. Jaudzems, K. Akopjana, I. Jirgensons, A. Tars, K. Tags: malaria proplasmepsin IV Plasmodium falciparum aspartic protease zymogen research communications Source Type: research
Surface-layer protein from Caulobacter crescentus: expression, purification and X-ray crystallographic analysis
Protein surface layers are self-assembling, paracrystalline lattices on the surface of many prokaryotes. Surface-layer proteins have not benefited from widespread structural analysis owing to their resistance to crystallization. Here, the successful expression of a truncated version of RsaA, the surface-layer protein from Caulobacter crescentus, from a Caulobacter protein-expression system is reported. The purification, crystallization and initial X-ray diffraction analysis of the truncated RsaA, the largest surface-layer protein studied to date and the first from a Gram-negative bacterium, are also reported. (Source: Acta...
Source: Acta Crystallographica Section F - August 9, 2016 Category: Biochemistry Authors: Jones, M.D. Chan, A.C.K. Nomellini, J.F. Murphy, M.E.P. Smit, J. Tags: S-layer surface-layer protein RTX motif phasing Gram-negative research communications Source Type: research
pHluorin-assisted expression, purification, crystallization and X-ray diffraction data analysis of the C-terminal domain of the HsdR subunit of the Escherichia coli type I restriction-modification system EcoR124I
The HsdR subunit of the type I restriction-modification system EcoR124I is responsible for the translocation as well as the restriction activity of the whole complex consisting of the HsdR, HsdM and HsdS subunits, and while crystal structures are available for the wild type and several mutants, the C-terminal domain comprising approximately 150 residues was not resolved in any of these structures. Here, three fusion constructs with the GFP variant pHluorin developed to overexpress, purify and crystallize the C-terminal domain of HsdR are reported. The shortest of the three encompassed HsdR residues 887 – 1038 and yie...
Source: Acta Crystallographica Section F - August 9, 2016 Category: Biochemistry Authors: Grinkevich, P. Iermak, I. Luedtke, N.A. Mesters, J.R. Ettrich, R. Ludwig, J. Tags: restriction-modification system EcoR124I HsdR pHluorin GFP Escherichia coli research communications Source Type: research
A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis
Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å , α = 90, β = 99.94, γ = 90 ° , and ...
Source: Acta Crystallographica Section F - August 7, 2016 Category: Biochemistry Authors: Trindade, I.B. Fonseca, B.M. Matias, P.M. Louro, R.O. Moe, E. Tags: siderophore-interacting protein Shewanella frigidimarina crystallographic analysis research communications Source Type: research
Crystal structure of AibC, a reductase involved in alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus
Isovaleryl coenzyme A (IV-CoA) performs a crucial role during development and fruiting-body formation in myxobacteria, which is reflected in the existence of a de novo biosynthetic pathway that is highly upregulated when leucine, the common precursor of IV-CoA, is limited. The final step in de novo IV-CoA biosynthesis is catalyzed by AibC, a medium-chain dehydrogenase/reductase. Here, the crystal structure of AibC from Myxococcus xanthus refined to 2.55 Å resolution is presented. The protein adopts two different conformations in the crystal lattice, which is a consequence of partial interaction with the purificat...
Source: Acta Crystallographica Section F - July 29, 2016 Category: Biochemistry Authors: Bock, T. M ü ller, R. Blankenfeldt, W. Tags: alternative isovaleryl coenzyme A biosynthesis medium-chain dehydrogenase/reductase zinc-dependence hexahistidine tag TEV protease-recognition sequence Myxococcus xanthus research communications Source Type: research
Characterization of the NTPR and BD1 interacting domains of the human PICH – BEND3 complex
Chromosome integrity depends on DNA structure-specific processing complexes that resolve DNA entanglement between sister chromatids. If left unresolved, these entanglements can generate either chromatin bridging or ultrafine DNA bridging in the anaphase of mitosis. These bridge structures are defined by the presence of the PICH protein, which interacts with the BEND3 protein in mitosis. To obtain structural insights into PICH – BEND3 complex formation at the atomic level, their respective NTPR and BD1 domains were cloned, overexpressed and crystallized using 1.56 M ammonium sulfate as a precipitant at pH 7.0. The...
Source: Acta Crystallographica Section F - July 27, 2016 Category: Biochemistry Authors: Pitchai, G.P. Hickson, I.D. Streicher, W. Montoya, G. Mesa, P. Tags: crystallization protein complex – protein interaction biophysics data collection research communications Source Type: research
Crystal structure of Rv3899c184 – 410, a hypothetical protein from Mycobacterium tuberculosis
Rv3899c is a hypothetical protein from Mycobacterium tuberculosis which is conserved across mycobacteria. It is predicted to be secreted and has been found in culture filtrates. It has been proposed as a potential vaccine candidate; however, its biological function is unknown. Here, the global structure of Rv3899c184 – 410, a fragment of Rv3899c, is reported. The structure resembles the shell of a sea snail, and its N- and C-termini form two relatively independent compact domains: an α / β / α sandwich folding domain and an α -helix bundle domain. There are no reported protein structures for an...
Source: Acta Crystallographica Section F - July 27, 2016 Category: Biochemistry Authors: Liu, Y. Gao, Y. Li, D. Fleming, J. Li, H. Bi, L. Tags: Mycobacterium tuberculosis Rv3899c184 – 410 crystal structure research communications Source Type: research
Crystal structure of the antigen-binding fragment of a monoclonal antibody specific for the multidrug-resistance-linked ABC transporter human P-glycoprotein
P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancers that plays important roles in the pharmacokinetics of a large number of drugs. The drug-resistance phenotype of P-gp can be modulated by the monoclonal antibody UIC2, which specifically recognizes human P-gp in a conformation-dependent manner. Here, the purification, sequence determination and high-resolution structure of the Fab fragment of UIC2 (UIC2/Fab) are reported. Purified UIC2/Fab binds human P-gp with a 1:1 stoichiometry. Crystals of UIC2/Fab are triclinic (space group P1), with unit-cell parameters a = 40.6...
Source: Acta Crystallographica Section F - July 27, 2016 Category: Biochemistry Authors: Esser, L. Shukla, S. Zhou, F. Ambudkar, S.V. Xia, D. Tags: monoclonal antibodies UIC2/Fab multidrug resistance human ABC-dependent transporter P-glycoprotein research communications Source Type: research
Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii
The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii were determined and their structural characteristics were analyzed. For PurS from T. thermophilus, two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date. A few residues were conserved among PurSs and these are located at the...
Source: Acta Crystallographica Section F - July 27, 2016 Category: Biochemistry Authors: Watanabe, Y. Yanai, H. Kanagawa, M. Suzuki, S. Tamura, S. Okada, K. Baba, S. Kumasaka, T. Agari, Y. Chen, L. Fu, Z.-Q. Chrzas, J. Wang, B.-C. Nakagawa, N. Ebihara, A. Masui, R. Kuramitsu, S. Yokoyama, S. Sampei, G. Kawai, G. Tags: purine nucleotide-biosynthetic pathway formylglycinamide ribonucleotide amidotransferase PurS crystal structure Thermus thermophilus Sulfolobus tokodaii Methanocaldococcus jannaschii research communications Source Type: research
Structural analysis of a function-associated loop mutant of the substrate-recognition domain of Fbs1 ubiquitin ligase
The SCF ubiquitin ligase comprises four components: Skp1, Cul1, Rbx1 and a variable-subunit F-box protein. The F-box protein Fbs1, which recognizes the N-linked glycoproteins, is involved in the endoplasmic reticulum-associated degradation pathway. Although FBG3, another F-box protein, shares 51% sequence identity with Fbs1, FBG3 does not bind glycoproteins. To investigate the sequence – structure relationship of the substrate-binding pocket, the crystal structure of a mutant substrate-binding domain of Fbs1 in which the six nonconserved regions ( β 1, β 2 – β 3, β 3 – β 4, β...
Source: Acta Crystallographica Section F - July 27, 2016 Category: Biochemistry Authors: Nishio, K. Yoshida, Y. Tanaka, K. Mizushima, T. Tags: SCF E3 ubiquitin ligase F-box protein glycoproteins sequence – structure relationship Fbs1 research communications Source Type: research
Structure of the lutein-binding domain of human StARD3 at 1.74 Å resolution and model of a complex with lutein
A crystal structure of the lutein-binding domain of human StARD3 (StAR-related lipid-transfer protein 3; also known as MLN64) has been refined to 1.74 Å resolution. A previous structure of the same protein determined to 2.2 Å resolution highlighted homology with StARD1 and shared cholesterol-binding character. StARD3 has since been recognized as a carotenoid-binding protein in the primate retina, where its biochemical function of binding lutein with specificity appears to be well suited to recruit this photoprotective molecule. The current and previous structures correspond closely to each other (r.m.s....
Source: Acta Crystallographica Section F - July 27, 2016 Category: Biochemistry Authors: Horvath, M.P. George, E.W. Tran, Q.T. Baumgardner, K. Zharov, G. Lee, S. Sharifzadeh, H. Shihab, S. Mattinson, T. Li, B. Bernstein, P.S. Tags: carotenoid-binding protein START domain StARD3 lutein protein tunnels and cavities research communications Source Type: research
Malonate in the nucleotide-binding site traps human AKAP18 γ / δ in a novel conformational state
A-kinase anchoring proteins (AKAPs) are a family of proteins that provide spatiotemporal resolution of protein kinase A (PKA) phosphorylation. In the myocardium, PKA and AKAP18 γ / δ are found in complex with sarcoendoplasmic reticulum Ca2+-ATPase 2 (SERCA2) and phospholamban (PLB). This macromolecular complex provides a means by which anchored PKA can dynamically regulate cytoplasmic Ca2+ release and re-uptake. For this reason, AKAP18 γ / δ presents an interesting drug target with therapeutic potential in cardiovascular disease. The crystal structure of the central domain of human AKAP18 γ ha...
Source: Acta Crystallographica Section F - July 13, 2016 Category: Biochemistry Authors: Bjerregaard-Andersen, K. Ø stensen, E. Scott, J.D. Task é n, K. Morth, J.P. Tags: A-kinase anchoring protein AKAP7 PKA phospholamban signalling drug design proton wire research communications Source Type: research
Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus
In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P21, with unit-cell parameters a = 106.07, b = 208.6...
Source: Acta Crystallographica Section F - July 13, 2016 Category: Biochemistry Authors: Rahman, M.M.Andberg, M.Koivula, A.Rouvinen, J.Hakulinen, N. Tags: l-arabinonate dehydratase d-xylonate dehydratase IlvD/EDD enzymes [Fe – S] cluster Rhizobium leguminosarum bv. trifolii Caulobacter crescentus research communications Source Type: research
Structure of the human DNA-repair protein RAD52 containing surface mutations
The Rad52 protein is a eukaryotic single-strand DNA-annealing protein that is involved in the homologous recombinational repair of DNA double-strand breaks. The isolated N-terminal half of the human RAD52 protein (RAD521–212) forms an undecameric ring structure with a surface that is mostly positively charged. In the present study, it was found that RAD521–212 containing alanine mutations of the charged surface residues (Lys102, Lys133 and Glu202) is highly amenable to crystallization. The structure of the mutant RAD521–212 was solved at 2.4 Å resolution. The structure revealed an association betw...
Source: Acta Crystallographica Section F - July 13, 2016 Category: Biochemistry Authors: Saotome, M.Saito, K.Onodera, K.Kurumizaka, H.Kagawa, W. Tags: ssDNA-binding protein single-strand annealing proteins homologous recombinational repair surface-entropy reduction higher order interaction RAD52 research communications Source Type: research
Malonate in the nucleotide-binding site traps human AKAP18γ/δ in a novel conformational state
A-kinase anchoring proteins (AKAPs) are a family of proteins that provide spatiotemporal resolution of protein kinase A (PKA) phosphorylation. In the myocardium, PKA and AKAP18γ/δ are found in complex with sarcoplasmatic reticulum Ca2+-ATPase 2 (SERCA2) and phospholamban (PLB). This macromolecular complex provides a means by which anchored PKA can dynamically regulate cytoplasmic Ca2+ release and re-uptake. For this reason, AKAP18γ/δ presents an interesting drug target with therapeutic potential in cardiovascular disease. The crystal structure of the central domain of human AKAP18γ has been de...
Source: Acta Crystallographica Section F - July 13, 2016 Category: Biochemistry Authors: Bjerregaard-Andersen, K.Østensen, E.Scott, J.D.Taskén, K.Morth, J.P. Tags: A-kinase anchoring protein AKAP7 PKA phospholamban signalling drug design proton wire research communications Source Type: research
Envelope protein VP24 from White spot syndrome virus: expression, purification and crystallization
White spot syndrome virus (WSSV) is a major shrimp pathogen known to infect penaeid shrimp and other crustaceans. VP24 is one of the major envelope proteins of WSSV. In order to facilitate purification, crystallization and structure determination, the predicted N-terminal transmembrane region of approximately 26 amino acids was truncated from VP24 and several mutants were prepared to increase the proportion of selenomethionine (SeMet) residues for subsequent structural determination using the SAD method. Truncated VP24, its mutants and the corresponding SeMet-labelled proteins were purified, and the native and SeMet protei...
Source: Acta Crystallographica Section F - July 13, 2016 Category: Biochemistry Authors: Sun, L.Wu, Y. Tags: White spot syndrome virus WSSV VP24 envelope protein purification crystallization research communications Source Type: research
Crystal structure of the PAS domain of the hEAG potassium channel
KCNH voltage-gated potassium channels play critical roles in regulating cellular functions. The channel is composed of four subunits, each of which contains six transmembrane helices forming the central pore. The cytoplasmic parts of the subunits present a Per–Arnt–Sim (PAS) domain at the N-terminus and a cyclic nucleotide-binding homology domain at the C-terminus. PAS domains are conserved from prokaryotes to eukaryotes and are involved in sensing signals and cellular responses. To better understand the functional roles of PAS domains in KCNH channels, the structure of this domain from the human ether-à...
Source: Acta Crystallographica Section F - July 12, 2016 Category: Biochemistry Authors: Tang, X.Shao, J.Qin, X. Tags: KCNH channels PAS domain ether- à -go-go channel hEAG potassium chanels research communications Source Type: research
Cryoannealing-induced space-group transition of crystals of the carbonic anhydrase psCA3
Cryoannealing has been demonstrated to improve the diffraction quality and resolution of crystals of the β-carbonic anhydrase psCA3 concomitant with a change in space group. After initial flash-cooling in a liquid-nitrogen cryostream an X-ray diffraction data set from a psCA3 crystal was indexed in space group P21212 and was scaled to 2.6 Å resolution, but subsequent cryoannealing studies revealed induced protein rearrangements in the crystal contacts, which transformed the space group to I222, with a corresponding improvement of 0.7 Å in resolution. Although the change in diffraction resolution was si...
Source: Acta Crystallographica Section F - June 28, 2016 Category: Biochemistry Authors: Pinard, M.A.Kurian, J.J.Aggarwal, M.Agbandje-McKenna, M.McKenna, R. Tags: β -carbonic anhydrase Pseudomonas aeruginosa cryoannealing crystal packing research communications Source Type: research
Crystallographic analysis of a subcomplex of the transsulfursome with tRNA for Cys-tRNACys synthesis
In this study, a subcomplex of the transsulfursome with tRNACys (SepCysS–SepCysE–tRNACys), which is involved in the second reaction step of the indirect pathway, was constructed and then crystallized. The crystals diffracted X-rays to a resolution of 2.6 Å and belonged to space group P6522, with unit-cell parameters a = b = 107.2, c = 551.1 Å. The structure determined by molecular replacement showed that the complex consists of a SepCysS dimer, a SepCysE dimer and one tRNACys in the asymmetric unit. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - June 28, 2016 Category: Biochemistry Authors: Chen, M.Nakazawa, Y.Kubo, Y.Asano, N.Kato, K.Tanaka, I.Yao, M. Tags: Cys-tRNACys SepRS SepCysS SepCysE transsulfursome research communications Source Type: research
The galactoside 2-α-l-fucosyltransferase FUT1 from Arabidopsis thaliana: crystallization and experimental MAD phasing
The plant cell wall is a complex network of polysaccharides made up of cellulose, hemicelluloses and pectins. Xyloglucan (XyG), which is the main hemicellulosic component of dicotyledonous plants, has attracted much attention for its role in plant development and for its many industrial applications. The XyG-specific fucosyltransferase (FUT1) adds a fucose residue from GDP-fucose to the 2-O position of the terminal galactosyl residues on XyG side chains. Recombinant FUT1 from Arabidopsis thaliana was crystallized in two different crystal forms, with the best diffracting crystals (up to 1.95 Å resolution) belonging ...
Source: Acta Crystallographica Section F - June 28, 2016 Category: Biochemistry Authors: Rocha, J.Cicéron, F.Lerouxel, O.Breton, C.de Sanctis, D. Tags: plant cell walls fucosyltransferase xyloglucan MAD tantalum bromide Arabidopsis thaliana research communications Source Type: research