1.2 Å resolution crystal structure of the periplasmic aminotransferase PvdN from Pseudomonas aeruginosa
This study reports the high-resolution structure of PvdN bound to a PLP cofactor solved by multi-wavelength anomalous dispersion (MAD). The PvdN model shows high structural homology to type I aspartate aminotransferases and also contains positive density that suggests an uncharacterized external aldimine. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Drake, E.J.Gulick, A.M. Tags: PvdN pyoverdine nonribosomal peptide synthetase Pseudomonas aeruginosa research communications Source Type: research

RRM domain of human RBM7: purification, crystallization and structure determination
RNA decay is an important process that is essential for controlling the abundance, quality and maturation of transcripts. In eukaryotes, RNA decay in the 3′–5′ direction is carried out by the exosome, an RNA-degradation machine that is conserved from yeast to humans. A range of cofactors stimulate the enzymatic activity of the exosome and serve as adapters for the many RNA substrates. In human cells, the exosome associates with the heterotrimeric nuclear exosome targeting (NEXT) complex consisting of the DExH-box helicase hMTR4, the zinc-finger protein hZCCHC8 and the RRM-type protein hRBM7. Here, the 2.5...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Sofos, N.Winkler, M.B.L.Brodersen, D.E. Tags: RNA degradation human NEXT complex RRM domain X-ray crystallography research communications Source Type: research

Structural and functional insights into the stationary-phase survival protein SurE, an important virulence factor of Brucella abortus
The stationary-phase survival protein SurE from Brucella abortus (BaSurE) is a metal-dependent phosphatase that is essential for the survival of this bacterium in the stationary phase of its life cycle. Here, BaSurE has been biochemically characterized and its crystal structure has been determined to a resolution of 1.9 Å. BaSurE was found to be a robust enzyme, showing activity over wide ranges of temperature and pH and with various phosphoester substrates. The active biomolecule is a tetramer and each monomer was found to consist of two domains: an N-terminal domain, which forms an approximate α + β fo...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Tarique, K.F.Abdul Rehman, S.A.Devi, S.Tomar, P.Gourinath, S. Tags: stationary-phase survival protein nucleotidase Brucella abortus phagosome domain swapping Rossmann fold malachite green assay research communications Source Type: research

The periplasmic sensing domain of Vibrio fischeri chemoreceptor protein A (VfcA): cloning, purification and crystallographic analysis
Flagella-mediated motility and chemotaxis towards nutrients are important characteristics of Vibrio fischeri that play a crucial role in the development of its symbiotic relationship with its Hawaiian squid host Euprymna scolopes. The V. fischeri chemoreceptor A (VfcA) mediates chemotaxis toward amino acids. The periplasmic sensory domain of VfcA has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 as a precipitating agent. The crystals belonged to space group P1, with unit-cell parameters a = 39.9, b = 57.0, c = 117.0 Å, α = 88.9, β = 80.5, γ =...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Salah Ud-Din, A.I.M.Roujeinikova, A. Tags: bacterial chemotaxis receptor sensing domain methyl-accepting protein research communications Source Type: research

Crystal structure of bile salt hydrolase from Lactobacillus salivarius
Bile salt hydrolase (BSH) is a gut-bacterial enzyme that negatively influences host fat digestion and energy harvesting. The BSH enzyme activity functions as a gateway reaction in the small intestine by the deconjugation of glycine-conjugated or taurine-conjugated bile acids. Extensive gut-microbiota studies have suggested that BSH is a key mechanistic microbiome target for the development of novel non-antibiotic food additives to improve animal feed production and for the design of new measures to control obesity in humans. However, research on BSH is still in its infancy, particularly in terms of the structural basis of ...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Xu, F.Guo, F.Hu, X.-J.Lin, J. Tags: bile salt hydrolase Lactobacillus lipid metabolism gut microbiome crystal structure research communications Source Type: research

Crystal structure of ketopantoate reductase from Thermococcus kodakarensis complexed with NADP+
Coenzyme A (CoA) plays pivotal roles in a variety of metabolic pathways in all organisms. The biosynthetic pathway of CoA is strictly regulated by feedback inhibition. In the hyperthermophilic archaeon Thermococcus kodakarensis, ketopantoate reductase (KPR), which catalyzes the NAD(P)H-dependent reduction of 2-oxopantoate, is a target of feedback inhibition by CoA. The crystal structure of KPR from T. kodakarensis (Tk-KPR) complexed with CoA and 2-oxopantoate has previously been reported. The structure provided an explanation for the competitive inhibition mechanism. Here, further biochemical analyses of Tk-KPR and the cry...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Aikawa, Y.Nishitani, Y.Tomita, H.Atomi, H.Miki, K. Tags: coenzyme A feedback inhibition competitive inhibition hyperthermophilic archaea research communications Source Type: research

Structural analysis of a phosphonate hydroxylase with an access tunnel at the back of the active site
FrbJ is a member of the Fe2+/α-ketoglutarate-dependent dioxygenase family which hydroxylates the natural product FR-900098 of Streptomyces rubellomurinus, yielding the phosphonate antibiotic FR-33289. Here, the crystal structure of FrbJ, which shows structural homology to taurine dioxygenase (TauD), a key member of the same family, is reported. Unlike other members of the family, FrbJ has an unusual lid structure which consists of two β-strands with a long loop between them. To investigate the role of this lid motif, a molecular-dynamics simulation was performed with the FrbJ structure. The molecular-dynamics si...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Li, C.Junaid, M.Almuqri, E.A.Hao, S.Zhang, H. Tags: FrbJ hydroxylase crystal structure access tunnel research communications Source Type: research

The Myb domain of LUX ARRHYTHMO in complex with DNA: expression, purification and crystallization
LUX ARRHYTHMO (LUX) is a Myb-domain transcription factor that plays an important role in regulating the circadian clock. Lux mutations cause severe clock defects and arrhythmia in constant light and dark. In order to examine the molecular mechanisms underlying the function of LUX, the DNA-binding Myb domain was cloned, expressed and purified. The DNA-binding activity of the Myb domain was confirmed using electrophoretic mobility shift assays (EMSAs), demonstrating that the LUX Myb domain is able to bind to DNA with nanomolar affinity. In order to investigate the specificity determinants of protein–DNA interactions, t...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Silva, C.S.Lai, X.Nanao, M.Zubieta, C. Tags: Myb domain DNA binding protein – DNA complex LUX ARRHYTHMO Arabidopsis thaliana research communications Source Type: research

Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library
Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Huschmann, F.U.Linnik, J.Sparta, K.Ühlein, M.Wang, X.Metz, A.Schiebel, J.Heine, A.Klebe, G.Weiss, M.S.Mueller, U. Tags: structural biology medicinal chemistry fragment screening X-ray crystallography protein – ligand structures research communications Source Type: research

Co-crystal structures of the protein kinase haspin with bisubstrate inhibitors
Haspin is a mitotic protein kinase that is responsible for the phosphorylation of Thr3 of histone H3, thereby creating a recognition motif for docking of the chromosomal passenger complex that is crucial for the progression of cell division. Here, two high-resolution models of haspin with previously reported inhibitors consisting of an ATP analogue and a histone H3(1–7) peptide analogue are presented. The structures of the complexes confirm the bisubstrate character of the inhibitors by revealing the signature binding modes of the moieties targeting the ATP-binding site and the protein substrate-binding site of the k...
Source: Acta Crystallographica Section F - April 21, 2016 Category: Biochemistry Authors: Lavogina, D.Kestav, K.Chaikuad, A.Heroven, C.Knapp, S.Uri, A. Tags: protein kinase haspin histone inhibitor bisubstrate linker research communications Source Type: research

Response to Errors in Crystal structure of HINT from Helicobacter pylori
A response is published to a Letter to the Editor by Maize [(2016), Acta Cryst. F72, 336-337]. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 23, 2016 Category: Biochemistry Authors: Tarique, K.F.Devi, S.Abdul Rehman, S.A.Gourinath, S. Tags: HINT PKCI letters to the editor Source Type: research

Errors in Crystal structure of HINT from Helicobacter pylori
Inaccuracies in the article, Crystal structure of HINT from Helicobacter pylori by Tarique et al. [(2016) Acta Cryst. F72, 42–48] are presented, and a brief history of HINT nomenclature is discussed. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 23, 2016 Category: Biochemistry Authors: Maize, K.M. Tags: HINT PKCI letters to the editor Source Type: research

Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site
The CotA laccase from Bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in a hole motif has been solved. The novel binding site was about 26 Å away from the T1 binding pocket. Comparison with known structures of other laccases revealed that the hole is a specific feature of CotA. The key residues Arg476 and Ser360 were directly bound to ABTS. Site-directed mutagenesis studies revealed that the residues Arg146, Arg429 and Arg476, which are located at ...
Source: Acta Crystallographica Section F - March 23, 2016 Category: Biochemistry Authors: Liu, Z.Xie, T.Zhong, Q.Wang, G. Tags: 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) laccase mutagenesis substrate binding protein engineering research communications Source Type: research

Crystal structure of a tankyrase 1–telomere repeat factor 1 complex
Telomere repeat factor 1 (TRF1) is a subunit of shelterin (also known as the telosome) and plays a critical role in inhibiting telomere elongation by telomerase. Tankyrase 1 (TNKS1) is a poly(ADP-ribose) polymerase that regulates the activity of TRF1 through poly(ADP-ribosyl)ation (PARylation). PARylation of TRF1 by TNKS1 leads to the release of TRF1 from telomeres and allows telomerase to access telomeres. The interaction between TRF1 and TNKS1 is thus important for telomere stability and the mitotic cell cycle. Here, the crystal structure of a complex between the N-terminal acidic domain of TRF1 (residues 1–55) and...
Source: Acta Crystallographica Section F - March 23, 2016 Category: Biochemistry Authors: Li, B.Qiao, R.Wang, Z.Zhou, W.Li, X.Xu, W.Rao, Z. Tags: TNKS tankyrase telomere TRF1 telomere repeat factor 1 PARylation complex structure research communications Source Type: research

Applications of thin-film sandwich crystallization platforms
Examples are shown of protein crystallization in, and data collection from, solutions sandwiched between thin polymer films using vapour-diffusion and batch methods. The crystallization platform is optimal for both visualization and in situ data collection, with the need for traditional harvesting being eliminated. In wells constructed from the thinnest plastic and with a minimum of aqueous liquid, flash-cooling to 100 K is possible without significant ice formation and without any degradation in crystal quality. The approach is simple; it utilizes low-cost consumables but yields high-quality data with minimal sample int...
Source: Acta Crystallographica Section F - March 23, 2016 Category: Biochemistry Authors: Axford, D.Aller, P.Sanchez-Weatherby, J.Sandy, J. Tags: protein crystallization devices in situ X-ray analysis crystal visual inspection diffraction data collection research communications Source Type: research

A novel microseeding method for the crystallization of membrane proteins in lipidic cubic phase
Random microseed matrix screening (rMMS), in which seed crystals are added to random crystallization screens, is an important breakthrough in soluble protein crystallization that increases the number of crystallization hits that are available for optimization. This greatly increases the number of soluble protein structures generated every year by typical structural biology laboratories. Inspired by this success, rMMS has been adapted to the crystallization of membrane proteins, making LCP seed stock by scaling up LCP crystallization conditions without changing the physical and chemical parameters that are critical for crys...
Source: Acta Crystallographica Section F - March 23, 2016 Category: Biochemistry Authors: Kolek, S.A.Bräuning, B.Shaw Stewart, P.D. Tags: membrane-protein crystallization microseeding lipidic cubic phase microseed matrix screening research communications Source Type: research

Crystal structure of histone-like protein from Streptococcus mutans refined to 1.9 Å resolution
Nucleoid-associated proteins (NAPs) in prokaryotes play an important architectural role in DNA bending, supercoiling and DNA compaction. In addition to architectural roles, some NAPs also play regulatory roles in DNA replication and repair, and act as global transcriptional regulators in many bacteria. Bacteria encode multiple NAPs and some of them are even essential for survival. Streptococcus mutans, a dental pathogen, encodes one such essential NAP called histone-like protein (HLP). Here, the three-dimensional structure of S. mutans HLP has been determined to 1.9 Å resolution. The HLP structure is a dimer and sh...
Source: Acta Crystallographica Section F - March 17, 2016 Category: Biochemistry Authors: O'Neil, P.Lovell, S.Mehzabeen, N.Battaile, K.Biswas, I. Tags: Streptococcus mutans HLP nucleoid-associated protein histone-like protein research communications Source Type: research

Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors
Leishmania arginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiates de novo polyamine biosynthesis by catalyzing the hydrolysis of l-arginine to generate l-ornithine and urea. The product l-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray cr...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Hai, Y.Christianson, D.W. Tags: Leishmania mexicana arginase α , -disubstituted boronic amino-acid inhibitors research communications Source Type: research

Purification, crystallization and X-ray diffraction analysis of the DNA-binding domain of human heat-shock factor 2
Cells respond to various proteotoxic stimuli and maintain protein homeostasis through a conserved mechanism called the heat-shock response, which is characterized by the enhanced synthesis of heat-shock proteins. This response is mediated by heat-shock factors (HSFs). Four genes encoding HSF1–HSF4 exist in the genome of mammals. In this protein family, HSF1 is the orthologue of the single HSF in lower eukaryotic organisms and is the major regulator of the heat-shock response, while HSF2, which shows low sequence homology to HSF1, serves as a developmental regulator. Increasing evidence has revealed biochemical proper...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Feng, H.Liu, W.Wang, D.-C. Tags: heat-shock factor DNA-binding domain transcription HSF2 research communications Source Type: research

Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17
Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, cr...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Godoy, A.S.de Lima, M.Z.T.Camilo, C.M.Polikarpov, I. Tags: galactanase Bifidobacterium GH43 family 43 hydrolase research communications Source Type: research

Isolation, crystallization and crystal structure determination of bovine kidney Na+,K+-ATPase
Na+,K+-ATPase is responsible for the transport of Na+ and K+ across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na+,K+-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na+,K+-ATPase in a high-affinity E2–BeF3−–ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one mol...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Gregersen, J.L.Mattle, D.Fedosova, N.U.Nissen, P.Reinhard, L. Tags: P-type ATPase native source isolation cardiotonic steroids Na ,K -ATPase ouabain research communications Source Type: research

Binding of Gd3+ to the neuronal signalling protein calexcitin identifies an exchangeable Ca2+-binding site
Calexcitin was first identified in the marine snail Hermissenda crassicornis as a neuronal-specific protein that becomes upregulated and phosphorylated in associative learning. Calexcitin possesses four EF-hand motifs, but only the first three (EF-1 to EF-3) are involved in binding metal ions. Past work has indicated that under physiological conditions EF-1 and EF-2 bind Mg2+ and Ca2+, while EF-3 is likely to bind only Ca2+. The fourth EF-hand is nonfunctional owing to a lack of key metal-binding residues. The aim of this study was to use a crystallographic approach to determine which of the three metal-binding sites of ca...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Chataigner, L.Guo, J.Erskine, P.T.Coker, A.R.Wood, S.P.Gombos, Z.Cooper, J.B. Tags: neuronal calcium signalling EF-hand protein structure heavy-atom complex co-crystallization research communications Source Type: research

Crystal structure of the substrate-recognition domain of the Shigella E3 ligase IpaH9.8
Infectious diseases caused by bacteria have significant impacts on global public health. During infection, pathogenic bacteria deliver a variety of virulence factors, called effectors, into host cells. The Shigella effector IpaH9.8 functions as an ubiquitin ligase, ubiquitinating the NF-κB essential modulator (NEMO)/IKK-γ to inhibit host inflammatory responses. IpaH9.8 contains leucine-rich repeats (LRRs) involved in substrate recognition and an E3 ligase domain. To elucidate the structural basis of the function of IpaH9.8, the crystal structure of the LRR domain of Shigella IpaH9.8 was determined and this stru...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Takagi, K.Kim, M.Sasakawa, C.Mizushima, T. Tags: Shigella flexneri effector leucine-rich repeats IpaH9.8 E3 ligase research communications Source Type: research

Cloning, expression, purification and crystallization of Schizosaccharomyces pombe Set7, a putative histone methyltransferase
Dysfunction of histone-modifying enzymes affects chromatin regulation and is involved in carcinogenesis, tumour progression and other diseases. Histone methyltransferases are a family of key histone-modifying enzymes, but their structures, functions and mechanisms are incompletely understood, thus constraining drug-design efforts. Here, preliminary steps towards structure–function studies of Schizosaccharomyces pombe Set7, a putative histone methyltransferase and the first yeast full-length SET-domain-containing protein to be studied using X-ray crystallography, are reported. The methods from cloning to X-ray diffrac...
Source: Acta Crystallographica Section F - March 16, 2016 Category: Biochemistry Authors: Mevius, D.E.H.F.Shen, Y.Morishita, M.di Luccio, E. Tags: histone modifications histone methyltransferase Schizosaccharomyces pombe Set7 X-ray crystallography research communications Source Type: research

Applications of the second virial coefficient: protein crystallization and solubility. Corrigendum
A number of citations in the article by Wilson & DeLucas [(2014). Acta Cryst. F70, 543–554] are corrected. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Wilson, W.W.DeLucas, L.J. Tags: second virial coefficient crystallization solubility corrigendum addenda and errata Source Type: research

Re-refinement of 4g4a: room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO
A re-refinement of 4g4a, the room-temperature X-ray diffraction study of cisplatin and its binding to His15 of HEWL after 14 months chemical exposure in the presence of DMSO is published as an addendum to Tanley et al. [(2012), Acta Cryst. F68, 1300–1306]. This example illustrates the benefits of sharing raw diffraction images, as well as structure factors and molecular coordinates, as the diffraction resolution of the study is now much improved at 1.70 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Tanley, S.W.M.Schreurs, A.M.M.Kroon-Batenburg, L.M.J.Helliwell, J.R. Tags: improved diffraction resolution raw diffraction images. re-refinement cisplatin histidine addendum addenda and errata Source Type: research

Re-refinement of 4xan: hen egg-white lysozyme with carboplatin in sodium bromide solution
A re-refinement of 4xan, hen egg-white lysozyme (HEWL) with carboplatin crystallized in NaBr solution, has been made and is published here as an addendum to Tanley et al. [(2014), Acta Cryst. F70, 1135–1142]. This follows a previous re-refinement and PDB deposition (4yem) by Shabalin et al. [(2015), Acta Cryst. D71, 1965–1979]. The critical evaluation of the original PDB deposition (4xan), and the subsequent critical examination of the re-refined structure (4yem), has led to an improved model (PDB code 5hmj). (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Tanley, S.W.M.Schreurs, A.M.M.Kroon-Batenburg, L.M.J.Helliwell, J.R. Tags: 4xan re-refinement raw diffraction data paired model refinement electron density assessment resolution limit assessment addendum addenda and errata Source Type: research

Crystal structure of recombinant tyrosinase-binding protein MtaL at 1.35 Å resolution
In this study, the crystal structure of recombinant MtaL is reported at 1.35 Å resolution. Comparison of its structure with that of the truncated and cleaved MtaL present in the complex with tyrosinase directly isolated from mushroom shows that the general β-trefoil fold is conserved. However, differences are detected in the loop regions, particularly in the β2–β3 loop, which is intact and not cleaved in the recombinant MtaL. Furthermore, the N-terminal tail is rotated inwards, covering the tyrosinase-binding interface. Thus, MtaL must undergo conformational changes in order to bind mature mush...
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Lai, X.Soler-Lopez, M.Ismaya, W.T.Wichers, H.J.Dijkstra, B.W. Tags: tyrosinase lectin tyrosinase-binding protein MtaL carbohydrate binding research communications Source Type: research

Crystallization and X-ray diffraction analysis of the CH domain of the cotton kinesin GhKCH2
GhKCH2 belongs to a group of plant-specific kinesins (KCHs) containing an actin-binding calponin homology (CH) domain in the N-terminus. Previous studies revealed that the GhKCH2 CH domain (GhKCH2-CH) had a higher affinity for F-actin (Kd = 0.42 ± 0.02 µM) than most other CH-domain-containing proteins. To understand the underlying mechanism, prokaryotically expressed GhKCH2-CH (amino acids 30–166) was purified and crystallized. Crystals were grown by the sitting-drop vapour-diffusion method using 0.1 M Tris–HCl pH 7.0, 20%(w/v) PEG 8000 as a precipitant. The crystals diffracted to a resolution ...
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Qin, X.Chen, Z.Li, P.Liu, G. Tags: plant-specific kinesin CH domain cotton kinesin GhKCH2 research communications Source Type: research

Purification, crystallization and initial crystallographic analysis of the α-catenin homologue HMP-1 from Caenorhabditis elegans
Adherens junctions transmit mechanical force between cells. In these junctions, β-catenin binds to cadherins and to the N-terminal domain of α-catenin, which in turn binds to actin filaments via its C-terminal domain. The middle (M) domain of α-catenin plays an important role in responding to mechanical tension. The nematode Caenorhabditis elegans contains α- and β-catenin homologues called HMP-1 and HMP-2, respectively, but HMP-1 behaves differently from its mammalian homologue. Thus, structural and biochemical studies of HMP-1 have been initiated to understand the mechanism of HMP-1 and the ev...
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Kang, H.Bang, I.Weis, W.I.Choi, H.-J. Tags: α -catenin HMP-1 adherens junction Caenorhabditis elegans research communications Source Type: research

Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine
Highly specific thymidine phosphorylases catalyze the phosphorolytic cleavage of thymidine, with the help of a phosphate ion, resulting in thymine and 2-deoxy-α-d-ribose 1-phosphate. Thymidine phosphorylases do not catalyze the phosphorolysis of uridine, in contrast to nonspecific pyrimidine nucleoside phosphorylases and uridine phosphorylases. Understanding the mechanism of substrate specificity on the basis of the nucleoside is essential to support rational drug-discovery investigations of new antitumour and anti-infective drugs which are metabolized by thymidine phosphorylases. For this reason, X-ray structures of...
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Balaev, V.V.Lashkov, A.A.Gabdulkhakov, A.G.Dontsova, M.V.Seregina, T.A.Mironov, A.S.Betzel, C.Mikhailov, A.M. Tags: X-ray analysis protein crystallography nucleoside phosphorylases nucleosides substrate specificity Salmonella typhimurium thymidine phosphorylase research communications Source Type: research

Neutron diffraction analysis of Pseudomonas aeruginosa peptidyl-tRNA hydrolase 1
Perdeuterated peptidyl-tRNA hydrolase 1 from Pseudomonas aeruginosa was crystallized for structural analysis using neutron diffraction. Crystals of perdeuterated protein were grown to 0.15 mm3 in size using batch crystallization in 22.5% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol with a 20-molar excess of trilysine as an additive. Neutron diffraction data were collected from a crystal at room temperature using the MaNDi single-crystal diffractometer at Oak Ridge National Laboratory. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: McFeeters, H.Vandavasi, V.G.Weiss, K.L.Coates, L.McFeeters, R.L. Tags: peptidyl-tRNA hydrolase 1 neutron diffraction perdeuteration Pseudomonas aeruginosa antibiotic resistance research communications Source Type: research

Crystal structure of FhuD at 1.6 Å resolution: a ferrichrome-binding protein from the animal and human pathogen Staphylococcus pseudintermedius
Staphylococcus pseudintermedius is a leading cause of disease in dogs, and zoonosis causes human infections. Methicillin-resistant S. pseudintermedius strains are emerging, resembling the global health threat of S. aureus. Therefore, it is increasingly important to characterize potential targets for intervention against S. pseudintermedius. Here, FhuD, an S. pseudintermedius surface lipoprotein implicated in iron uptake, was characterized. It was found that FhuD bound ferrichrome in an iron-dependent manner, which increased the thermostability of FhuD by>15°C. The crystal structure of ferrichrome-free FhuD was deter...
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Abate, F.Cozzi, R.Maritan, M.Lo Surdo, P.Maione, D.Malito, E.Bottomley, M.J. Tags: metal transport staphylococcal disease siderophore iron class III solute-binding protein research communications Source Type: research

Purification, crystallization and X-ray crystallographic analysis of a putative exopolyphosphatase from Zymomonas mobilis
In this study, a putative exopolyphosphatase from Zymomonas mobilis (ZmPPX) was crystallized. Crystals of the wild-type enzyme diffracted to 3.3 Å resolution and could not be optimized further. The truncation of 29 amino acids from the N-terminus resulted in crystals that diffracted to 1.8 Å resolution. The crystals belonged to space group C2, with unit-cell parameters a = 122.0, b = 47.1, c = 89.5 Å, α = γ = 90, β = 124.5°. An active-site mutant that crystallized in the same space group and with similar unit-cell parameters diffracted to 1.56 Å resolution. One molecule ...
Source: Acta Crystallographica Section F - February 19, 2016 Category: Biochemistry Authors: Zhang, A.Guo, E.Qian, L.Tang, N.-Y.Watt, R.M.Bartlam, M. Tags: exopolyphosphatase PPX/GppA family crystallization Zymomonas mobilis research communications Source Type: research

Crystal structure of recombinant tyrosinase-binding protein MtaL at 1.35   Å resolution
In this study, the crystal structure of recombinant MtaL is reported at 1.35   Å resolution. Comparison of its structure with that of the truncated and cleaved MtaL present in the complex with tyrosinase directly isolated from mushroom shows that the general β -trefoil fold is conserved. However, differences are detected in the loop regions, particularly in the β 2 – β 3 loop, which is intact and not cleaved in the recombinant MtaL. Furthermore, the N-terminal tail is rotated inwards, covering the tyrosinase-binding interface. Thus, MtaL must undergo conformational changes in order to bind matu...
Source: Acta Crystallographica Section F - February 18, 2016 Category: Biochemistry Authors: Lai, X. Soler-Lopez, M. Ismaya, W.T. Wichers, H.J. Dijkstra, B.W. Tags: tyrosinase lectin tyrosinase-binding protein MtaL carbohydrate binding research communications Source Type: research

Purification, crystallization and initial crystallographic analysis of the α -catenin homologue HMP-1 from Caenorhabditis elegans
Adherens junctions transmit mechanical force between cells. In these junctions, β -catenin binds to cadherins and to the N-terminal domain of α -catenin, which in turn binds to actin filaments via its C-terminal domain. The middle (M) domain of α -catenin plays an important role in responding to mechanical tension. The nematode Caenorhabditis elegans contains α - and β -catenin homologues called HMP-1 and HMP-2, respectively, but HMP-1 behaves differently from its mammalian homologue. Thus, structural and biochemical studies of HMP-1 have been initiated to understand the mechanism of HMP-1 and t...
Source: Acta Crystallographica Section F - February 18, 2016 Category: Biochemistry Authors: Kang, H. Bang, I. Weis, W.I. Choi, H.-J. Tags: α -catenin HMP-1 adherens junction Caenorhabditis elegans research communications Source Type: research

Crystal structure of FhuD at 1.6   Å resolution: a ferrichrome-binding protein from the animal and human pathogen Staphylococcus pseudintermedius
Staphylococcus pseudintermedius is a leading cause of disease in dogs, and zoonosis causes human infections. Methicillin-resistant S. pseudintermedius strains are emerging, resembling the global health threat of S. aureus. Therefore, it is increasingly important to characterize potential targets for intervention against S. pseudintermedius. Here, FhuD, an S. pseudintermedius surface lipoprotein implicated in iron uptake, was characterized. It was found that FhuD bound ferrichrome in an iron-dependent manner, which increased the thermostability of FhuD by>15 ° C. The crystal structure of ferrichrome-free FhuD was det...
Source: Acta Crystallographica Section F - February 18, 2016 Category: Biochemistry Authors: Abate, F. Cozzi, R. Maritan, M. Lo Surdo, P. Maione, D. Malito, E. Bottomley, M.J. Tags: metal transport staphylococcal disease siderophore iron class III solute-binding protein research communications Source Type: research

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human C1ORF123 protein
C1ORF123 is a human hypothetical protein found in open reading frame 123 of chromosome 1. The protein belongs to the DUF866 protein family comprising eukaryote-conserved proteins with unknown function. Recent proteomic and bioinformatic analyses identified the presence of C1ORF123 in brain, frontal cortex and synapses, as well as its involvement in endocrine function and polycystic ovary syndrome (PCOS), indicating the importance of its biological role. In order to provide a better understanding of the biological function of the human C1ORF123 protein, the characterization and analysis of recombinant C1ORF123 (rC1ORF123), ...
Source: Acta Crystallographica Section F - February 16, 2016 Category: Biochemistry Authors: Rahaman, S.N.A.Mat Yusop, J.Mohamed-Hussein, Z.-A.Ho, K.L.Teh, A.-H.Waterman, J.Ng, C.L. Tags: C1ORF123 hypothetical protein DUF866 polycystic ovary syndrome bioinformatic analysis research communications Source Type: research

Structure of a truncated form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement
This study highlights that N-terminal truncation of LZII can change its coiled-coil orientation without affecting its overall stability. Further, a conserved buried asparagine residue was pinpointed as a possible structural determinant for this dramatic structural rearrangement. Thus, LZII of JIP3/4 is a versatile structural motif, modifications of which can impact partner recognition and thus biological function. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 16, 2016 Category: Biochemistry Authors: Llinas, P.Chenon, M.Nguyen, T.Q.Moreira, C.de Régibus, A.Coquard, A.Ramos, M.J.Guérois, R.Fernandes, P.A.Ménétrey, J. Tags: JIP3 JIP4 leucine zipper II crystal structure molecular dynamics antiparallel coiled coil buried asparagine research communications Source Type: research

The use of noncrystallographic symmetry averaging to solve structures from data affected by perfect hemihedral twinning
Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of the domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) av...
Source: Acta Crystallographica Section F - February 16, 2016 Category: Biochemistry Authors: Sabin, C.Plevka, P. Tags: hemihedral perfect twinning noncrystallographic symmetry averaging molecular replacement virus structure detwinning twin domain merohedral twinning mask envelope research communications Source Type: research

Crystal structure of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase from the ESKAPE pathogen Acinetobacter baumannii
The enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes the sixth step of the seven-step shikimate pathway. Chorismate, the product of the pathway, is a precursor for the biosynthesis of aromatic amino acids, siderophores and metabolites such as folate, ubiquinone and vitamin K. The shikimate pathway is present in bacteria, fungi, algae, plants and apicomplexan parasites, but is absent in humans. The EPSP synthase enzyme produces 5-enolpyruvylshikimate 3-phosphate and phosphate from phosphoenolpyruvate and shikimate 3-phosphate via a transferase reaction, and is the target of the herbicide glyphosate. The A...
Source: Acta Crystallographica Section F - February 16, 2016 Category: Biochemistry Authors: Sutton, K.A.Breen, J.Russo, T.A.Schultz, L.W.Umland, T.C. Tags: shikimate pathway Acinetobacter baumannii essential genes antibiotic targets multidrug resistance EPSP synthase research communications Source Type: research

Crystal structure of maize serine racemase with pyridoxal 5′-phosphate
Serine racemase (SR) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that is responsible for d-serine biosynthesis in vivo. The first X-ray crystal structure of maize SR was determined to 2.1 Å resolution and PLP binding was confirmed in solution by UV–Vis absorption spectrometry. Maize SR belongs to the type II PLP-dependent enzymes and differs from the SR of a vancomycin-resistant bacterium. The PLP is bound to each monomer by forming a Schiff base with Lys67. Structural comparison with rat and fission yeast SRs reveals a similar arrangement of active-site residues but a different orientation of th...
Source: Acta Crystallographica Section F - February 16, 2016 Category: Biochemistry Authors: Zou, L.Song, Y.Wang, C.Sun, J.Wang, L.Cheng, B.Fan, J. Tags: structural comparison serine racemase maize crystal structure cofactor pyridoxal 5 ′ -phosphate research communications Source Type: research

Crystal structure of maize serine racemase with pyridoxal 5 ′ -phosphate
Serine racemase (SR) is a pyridoxal 5 ′ -phosphate (PLP)-dependent enzyme that is responsible for d-serine biosynthesis in vivo. The first X-ray crystal structure of maize SR was determined to 2.1   Å resolution and PLP binding was confirmed in solution by UV – Vis absorption spectrometry. Maize SR belongs to the type II PLP-dependent enzymes and differs from the SR of a vancomycin-resistant bacterium. The PLP is bound to each monomer by forming a Schiff base with Lys67. Structural comparison with rat and fission yeast SRs reveals a similar arrangement of active-site residues but a different orientation...
Source: Acta Crystallographica Section F - February 15, 2016 Category: Biochemistry Authors: Zou, L. Song, Y. Wang, C. Sun, J. Wang, L. Cheng, B. Fan, J. Tags: structural comparison serine racemase maize crystal structure cofactor pyridoxal 5 ′ -phosphate research communications Source Type: research

Crystal structure of human GDF11
Members of the TGF-β family of proteins are believed to play critical roles in cellular signaling processes such as those involved in muscle differentiation. The extent to which individual family members have been characterized and linked to biological function varies greatly. The role of myostatin, also known as growth differentiation factor 8 (GDF8), as an inhibitor of muscle differentiation is well understood through genetic linkages. In contrast, the role of growth differentiation factor 11 (GDF11) is much less well understood. In humans, the mature forms of GDF11 and myostatin are over 94% identical. In order to ...
Source: Acta Crystallographica Section F - February 15, 2016 Category: Biochemistry Authors: Padyana, A.K.Vaidialingam, B.Hayes, D.B.Gupta, P.Franti, M.Farrow, N.A. Tags: growth differentiation factor 11 GDF11 TGF- β family research communications Source Type: research

Improving diffraction resolution using a new dehydration method
The production of high-quality crystals is one of the major obstacles in determining the three-dimensional structure of macromolecules by X-ray crystallography. It is fairly common that a visually well formed crystal diffracts poorly to a resolution that is too low to be suitable for structure determination. Dehydration has proven to be an effective post-crystallization treatment for improving crystal diffraction quality. Several dehydration methods have been developed, but no single one of them is suitable for all crystals. Here, a new convenient and effective dehydration method is reported that makes use of a dehydrating...
Source: Acta Crystallographica Section F - January 28, 2016 Category: Biochemistry Authors: Huang, Q.Szebenyi, D.M.E. Tags: protein crystal dehydration diffraction resolution Cas5a LptA research communications Source Type: research

Protein stability: a crystallographer's perspective
Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along...
Source: Acta Crystallographica Section F - January 28, 2016 Category: Biochemistry Authors: Deller, M.C.Kong, L.Rupp, B. Tags: protein stability protein crystallization protein disorder crystallizability research communications Source Type: research

Crystallization and X-ray diffraction of LGN in complex with the actin-binding protein afadin
Asymmetric stem-cell divisions are fundamental for morphogenesis and tissue homeostasis. They rely on the coordination between cortical polarity and the orientation of the mitotic spindle, which is orchestrated by microtubule pulling motors recruited at the cortex by NuMA–LGN–Gαi complexes. LGN has emerged as a central component of the spindle-orientation pathway that is conserved throughout species. Its domain structure consists of an N-terminal TPR domain associating with NuMA, followed by four GoLoco motifs binding to Gαi subunits. The LGNTPR region is also involved in interactions with other mem...
Source: Acta Crystallographica Section F - January 26, 2016 Category: Biochemistry Authors: Carminati, M.Cecatiello, V.Mapelli, M. Tags: LGN spindle orientation fusion proteins research communications Source Type: research

The role of mass transport in protein crystallization
Mass transport takes place within the mesoscopic to macroscopic scale range and plays a key role in crystal growth that may affect the result of the crystallization experiment. The influence of mass transport is different depending on the crystallization technique employed, essentially because each technique reaches supersaturation in its own unique way. In the case of batch experiments, there are some complex phenomena that take place at the interface between solutions upon mixing. These transport instabilities may drastically affect the reproducibility of crystallization experiments, and different outcomes may be obtaine...
Source: Acta Crystallographica Section F - January 26, 2016 Category: Biochemistry Authors: García-Ruiz, J.M.Otálora, F.García-Caballero, A. Tags: mass transport crystal growth protein crystallization research communications Source Type: research

Crystallographic observation of the movement of the membrane-distal domain of the T7SS core component EccB1 from Mycobacterium tuberculosis
The protein EccB1, a core component of the type VII secretion system (T7SS) of Mycobacterium tuberculosis, has been identified as an ATPase and is essential for the secretion of virulence factors by the ESX-1 system. In a previous study, EccB1 structures were determined in two different conformations. Here, two new conformations are identified and described. These four conformations present snapshots of the swinging movement of the membrane-distal domain A2. The movement of this domain involves conformational changes in two flexible loops (loop A, residues 243–264, and loop B, residues 324–341) which are rich i...
Source: Acta Crystallographica Section F - January 22, 2016 Category: Biochemistry Authors: Xie, X.-Q.Zhang, X.-L.Qi, C.Li, D.-F.Fleming, J.Wang, D.-C.Bi, L.-J. Tags: Rv3869 type VII secretion system Mycobacterium tuberculosis ESX-1 research communications Source Type: research

Cloning, expression, purification, crystallization and initial crystallographic analysis of FleN from Pseudomonas aeruginosa
The assembly of bacterial flagella requires the coordinated expression of a large number of genes in a hierarchical manner. These genes code for structural components of flagella, regulatory components and components that are required for chemotaxis. Stringent spatial and numerical control of flagella biosynthesis is essential for promoting motility and pathogenesis in bacteria. These genes are regulated at the level of transcription. FleN, a P-loop-containing ATPase, plays an important role in maintaining flagellar number in Pseudomonas aeruginosa. FleN exhibits anti-activator activity against FleQ, the global transcripti...
Source: Acta Crystallographica Section F - January 22, 2016 Category: Biochemistry Authors: HarshitaChanchalJain, D. Tags: FleN transcription flagella Pseudomonas research communications Source Type: research