Structural basis of the substrate specificity of the FPOD/FAOD family revealed by fructosyl peptide oxidase from Eupenicillium terrenum
This study reveals the first structural details of group I FPODs that prefer α-fructosyl substrates and could provide significant useful information for uncovering the mechanism of substrate specificity of FAOD/FPODs and guidance towards future enzyme engineering for diagnostic purposes. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Gan, W.Gao, F.Xing, K.Jia, M.Liu, H.Gong, W. Tags: fructosyl peptide oxidase Eupenicillium terrenum FAOD/FPOD family research communications Source Type: research

Crystallization of mutants of Turnip yellow mosaic virus protease/ubiquitin hydrolase designed to prevent protease self-recognition
Processing of the polyprotein of Turnip yellow mosaic virus is mediated by the protease PRO. PRO cleaves at two places, one of which is at the C-terminus of the PRO domain of another polyprotein molecule. In addition to this processing activity, PRO possesses an ubiquitin hydrolase (DUB) activity. The crystal structure of PRO has previously been reported in its polyprotein-processing mode with the C-terminus of one PRO inserted into the catalytic site of the next PRO, generating PRO polymers in the crystal packing of the trigonal space group. Here, two mutants designed to disrupt specific PRO–PRO interactions were ge...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Ayach, M.Bressanelli, S. Tags: self-processing viral cysteine proteinase ubiquitin hydrolase research communications Source Type: research

The X-ray structure of human P-cadherin EC1-EC2 in a closed conformation provides insight into the type I cadherin dimerization pathway
Cadherins are a large family of calcium-dependent proteins that mediate cellular adherens junction formation and tissue morphogenesis. To date, the most studied cadherins are those classified as classical, which are further divided into type I or type II depending on selected sequence features. Unlike other members of the classical cadherin family, a detailed structural characterization of P-cadherin has not yet been fully obtained. Here, the high-resolution crystal structure determination of the closed form of human P-cadherin EC1-EC2 is reported. The structure shows a novel, monomeric packing arrangement that provides a ...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Dalle Vedove, A.Lucarelli, A.P.Nardone, V.Matino, A.Parisini, E. Tags: cadherin dimerization mechanism cell adhesion research communications Source Type: research

Purification, crystallization and preliminary X-ray analysis of the periplasmic haem-binding protein HutB from Vibrio cholerae
The mechanism of haem transport across the inner membrane of pathogenic bacteria is currently insufficiently understood at the molecular level and no information is available for this process in Vibrio cholerae. To obtain structural insights into the periplasmic haem-binding protein HutB from V. cholerae (VcHutB), which is involved in haem transport through the HutBCD haem-transport system, at the atomic level, VcHutB was cloned, overexpressed and crystallized using 1.6 M ammonium sulfate as a precipitant at pH 7.0. X-ray diffraction data were collected to 2.4 Å resolution on the RRCAT PX-BL-21 beamline at the In...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Agarwal, S.Biswas, M.Dasgupta, J. Tags: Vibrio cholerae iron uptake periplasmic haem-binding protein ABC transporter research communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of an endo-1,4-β-d-glucanase from Aspergillus aculeatus F-50
Cellulose is the most abundant renewable biomass on earth, and its decomposition has proven to be very useful in a wide variety of industries. Endo-1,4-β-d-glucanase (EC 3.2.1.4; endoglucanase), which can catalyze the random hydrolysis of β-1,4-glycosidic bonds to cleave cellulose into smaller fragments, is a key cellulolytic enzyme. An endoglucanase isolated from Aspergillus aculeatus F-50 (FI-CMCase) that was classified into glycoside hydrolase family 12 has been found to be effectively expressed in the industrial strain Pichia pastoris. Here, recombinant FI-CMCase was crystallized. Crystals belonging to the or...
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Chen, Y.Huang, J.-W.Chen, C.-C.Lai, H.-L.Jin, J.Guo, R.-T. Tags: cellulase endoglucanase Aspergillus industrial enzyme research communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the interaction of Aeromonas hydrophila MtaN-1 with S-adenosylhomocysteine
In this study, MtaN-1 from Aeromonas hydrophila was successfully expressed and purified using Ni–NTA affinity, Q anion-exchange and gel-filtration chromatography. Crystals of the protein in complex with the substrate SAH were obtained and diffracted to a resolution of 1.4 Å. The crystals belonged to the trigonal space group P3121 or P3221, with unit-cell parameters a = b = 102.7, c = 118.8 Å. The asymmetric unit contained two molecules of MtaN-1 complexed with SAH. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 20, 2015 Category: Biochemistry Authors: Xu, Y.Quan, C.-S.Jin, X.Jin, X.Zhao, J.Jin, L.Kim, J.-S.Guo, J.Fan, S.Ha, N.-C. Tags: Aeromonas hydrophila MtaN-1 S-adenosylmethionine research communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of the sclerostin-neutralizing Fab AbD09097
The secreted cystine-knot protein sclerostin was first identified from genetic screening of patients suffering from the rare bone-overgrowth diseases sclerosteosis and van Buchem disease. Sclerostin acts a negative regulator of bone growth through inhibiting the canonical Wnt signalling cascade by binding to and blocking the Wnt co-receptor LRP5/6. Its function in blocking osteoblastogenesis makes it an important target for osteoanabolic therapy approaches to treat osteoporosis, which is characterized by a progressive decrease in bone mass and density. In this work, the production, crystallization and preliminary X-ray dif...
Source: Acta Crystallographica Section F - March 19, 2015 Category: Biochemistry Authors: Boschert, V.Muth, E.-M.Knappik, A.Frisch, C.Mueller, T.D. Tags: Wnt signalling pathway sclerostin bone homeostasis osteoporosis research communications Source Type: research

Crystallization and preliminary X-ray analysis of Rv1674c from Mycobacterium tuberculosis
Adaptations to hypoxia play an important role in Mycobacterium tuberculosis pathogenesis. Rv0324, which contains an HTH DNA-binding domain and a rhodanese domain, is one of the key transcription regulators in response to hypoxia. M. tuberculosis Rv1674c is a homologue of Rv0324. To understand the interdomain interaction and regulation of the HTH domain and the rhodanese domain, recombinant Rv1674c protein was purified and crystallized by the vapour-diffusion method. The crystals diffracted to 2.25 Å resolution. Preliminary diffraction analysis suggests that the crystals belonged to space group P3121 or P3221, with ...
Source: Acta Crystallographica Section F - February 28, 2015 Category: Biochemistry Authors: Li, J.Wang, X.Gong, W.Niu, C.Zhang, M. Tags: Rv1674c HTH DNA-binding domain rhodanese domain research communications Source Type: research

Origin and use of crystallization phase diagrams
Crystallization phase diagrams are frequently used to conceptualize the phase relations and also the processes taking place during the crystallization of macromolecules. While a great deal of freedom is given in crystallization phase diagrams owing to a lack of specific knowledge about the actual phase boundaries and phase equilibria, crucial fundamental features of phase diagrams can be derived from thermodynamic first principles. Consequently, there are limits to what can be reasonably displayed in a phase diagram, and imagination may start to conflict with thermodynamic realities. Here, the commonly used `crystallizatio...
Source: Acta Crystallographica Section F - February 27, 2015 Category: Biochemistry Authors: Rupp, B. Tags: crystallization phase diagrams non-ideal mixtures thermodynamics excess properties research communications Source Type: research

Improved crystallization and diffraction of caffeine-induced death suppressor protein 1 (Cid1)
The post-transcriptional addition of uridines to the 3′-end of RNAs is an important regulatory process that is critical for coding and noncoding RNA stability. In fission yeast and metazoans this untemplated 3′-uridylylation is catalysed by a single family of terminal uridylyltransferases (TUTs) whose members are adapted to specific RNA targets. In Schizosaccharomyces pombe the TUT Cid1 is responsible for the uridylylation of polyadenylated mRNAs, targeting them for destruction. In metazoans, the Cid1 orthologues ZCCHC6 and ZCCHC11 uridylate histone mRNAs, targeting them for degradation, but also uridylate micr...
Source: Acta Crystallographica Section F - February 21, 2015 Category: Biochemistry Authors: Yates, L.A.Durrant, B.P.Barber, M.Harlos, K.Fleurdépine, S.Norbury, C.J.Gilbert, R.J.C. Tags: terminal uridylyltransferases Cid1 research communications Source Type: research

High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-l-arabinofuranosidase activity
A gene from the heterotrophic, halothermophilic marine bacterium Halothermothrix orenii has been cloned and overexpressed in Escherichia coli. This gene encodes the only glycoside hydrolase of family 43 (GH43) produced by H. orenii. The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. As for other GH43 members, the enzyme folds as a five-bladed β-propeller. The structure features a metal-binding site on the propeller axis, near the active site. Based on thermal denaturation data, the H. orenii glycosidase depends on divalent cations in com...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Hassan, N.Kori, L.D.Gandini, R.Patel, B.K.C.Divne, C.Tan, T.C. Tags: glycoside hydrolase five-bladed β -propeller arabinofuranosidase Halothermothrix orenii halothermophile research communications Source Type: research

Crystallization and preliminary X-ray analysis of the Plasmodium falciparum apicoplast DNA polymerase
Infection by the parasite Plasmodium falciparum is the leading cause of malaria in humans. The parasite has a unique and essential plastid-like organelle called the apicoplast. The apicoplast contains a genome that undergoes replication and repair through the action of a replicative polymerase (apPOL). apPOL has no direct orthologs in mammalian polymerases and is therefore an attractive antimalarial drug target. No structural information exists for apPOL, and the Klenow fragment of Escherichia coli DNA polymerase I, which is its closest structural homolog, shares only 28% sequence identity. Here, conditions for the crystal...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Milton, M.E.Choe, J.Honzatko, R.B.Nelson, S.W. Tags: DNA polymerase apicoplast Plasmodium falciparum research communications Source Type: research

Protein production, crystallization and preliminary X-ray analysis of two isoforms of the Dscam1 Ig7 domain
Drosophila Down syndrome cell adhesion molecule 1 (Dscam1) plays a critical role in neural development. It can potentially form 38 016 isoforms through alternative RNA splicing, and exhibits isoform-specific homophilic interaction through three variable Ig domains (Ig2, Ig3 and Ig7). The diversity and homophilic interaction are essential for its functions. Ig7 has 33 isoforms and is the most variable among the three variable Ig domains. However, only one isoform of Ig7 (isoform 30) has been structurally determined to date. Here, two isoforms of Dscam1 Ig7 (isoforms 5 and 9; Ig75 and Ig79) were produced and crystallized. ...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Li, S.-A.Cheng, L.Yu, Y.Chen, Q. Tags: Dscam1 RNA splicing Ig7 homophilic dimer research communications Source Type: research

Bacterial expression and preliminary crystallographic studies of a 149-residue fragment of human Caprin-1
Caprin-1 is an RNA-binding protein which plays critical roles in several important biological processes, including cellular proliferation, the interferon-mediated antiviral innate immune response, the maintenance of synaptic plasticity and the formation of RNA stress granules. Caprin-1 has been implicated in the pathogenesis of several human diseases, including osteosarcoma, breast cancer, viral infections, hearing loss and neurodegenerative disorders. Despite the emerging biological and physiopathological significance of Caprin-1, no structural information is available for this protein. Moreover, Caprin-1 does not have se...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Wu, Y.Zhu, J.Huang, X.Du, Z. Tags: Caprin-1 Caprin-2 G3BP1 Pou4f3 JEV core protein DENV-2 sfRNA research communications Source Type: research

Crystallization and preliminary crystallographic analysis of acetophenone reductase from Geotrichum candidum NBRC 4597
Acetophenone reductase (APRD) from Geotrichum candidium NBRC 4597 was crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as a precipitant. The crystal belonged to space group P6522, with unit-cell parameters a = b = 104.5, c = 273.7 Å, and diffracted to 2.6 Å resolution. Phasing using the single-wavelength anomalous diffraction method was successful. Model building and crystallographic refinement are in progress. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Sugiyama, Y.Senda, M.Senda, T.Matsuda, T. Tags: acetophenone reductase enantioselectivity asymmetric reduction research communications Source Type: research

The structure of C290A:C393A Aurora A provides structural insights into kinase regulation
Aurora A is a Ser/Thr protein kinase that functions in cell-cycle regulation and is implicated in cancer development. During mitosis, Aurora A is activated by autophosphorylation on its activation loop at Thr288. The Aurora A catalytic domain (amino acids 122–403) expressed in Escherichia coli autophosphorylates on two activation-loop threonine residues (Thr288 and Thr287), whereas a C290A,C393A double point mutant of the Aurora A catalytic domain autophosphorylates only on Thr288. The structure of the complex of this mutant with ADP and magnesium was determined to 2.1 Å resolution using molecular replacement...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Burgess, S.G.Bayliss, R. Tags: protein kinase phosphorylation activation research communications Source Type: research

Cloning, purification, crystallization and preliminary X-ray studies of a carbohydrate-binding module from family 64 (StX)
In recent years, biofuels have attracted great interest as a source of renewable energy owing to the growing global demand for energy, the dependence on fossil fuels, limited natural resources and environmental pollution. However, the cost-effective production of biofuels from plant biomass is still a challenge. In this context, the study of carbohydrate-binding modules (CBMs), which are involved in guiding the catalytic domains of glycoside hydrolases to polysaccharides, is crucial for enzyme development. Aiming at the structural and functional characterization of novel CBMs involved in plant polysaccharide deconstruction...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Campos, B.M.Liberato, M.V.Polikarpov, I.Zeri, A.C.M.Squina, F.M. Tags: accessory domain carbohydrate-binding module research communications Source Type: research

Mode of binding of the antithyroid drug propylthiouracil to mammalian haem peroxidases
The mammalian haem peroxidase superfamily consists of myeloperoxidase (MPO), lactoperoxidase (LPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). These enzymes catalyze a number of oxidative reactions of inorganic substrates such as Cl−, Br−, I− and SCN− as well as of various organic aromatic compounds. To date, only structures of MPO and LPO are known. The substrate-binding sites in these enzymes are located on the distal haem side. Propylthiouracil (PTU) is a potent antithyroid drug that acts by inhibiting the function of TPO. It has also been shown to inhibit the action of LPO. Howeve...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Singh, R.P.Singh, A.Kushwaha, G.S.Singh, A.K.Kaur, P.Sharma, S.Singh, T.P. Tags: lactoperoxidase propylthiouracil distal haem side antithyroid drug research communications Source Type: research

Cwp84, a Clostridium difficile cysteine protease, exhibits conformational flexibility in the absence of its propeptide
In recent decades, the global healthcare problems caused by Clostridium difficile have increased at an alarming rate. A greater understanding of this antibiotic-resistant bacterium, particularly with respect to how it interacts with the host, is required for the development of novel strategies for fighting C. difficile infections. The surface layer (S-layer) of C. difficile is likely to be of significant importance to host–pathogen interactions. The mature S-layer is formed by a proteinaceous array consisting of multiple copies of a high-molecular-weight and a low-molecular-weight S-layer protein. These components re...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Bradshaw, W.J.Roberts, A.K.Shone, C.C.Acharya, K.R. Tags: Clostridium difficile surface layer Cwp84 host – pathogen interactions research communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the arginine repressor ArgR from Bacillus halodurans
The arginine repressor (ArgR) is a transcriptional regulator which regulates genes encoding proteins involved in arginine biosynthesis and the arginine catabolic pathway. ArgR from the alkaliphilic bacterium Bacillus halodurans was cloned and overexpressed in Escherichia coli. ArgR (Bh2777) from B. halodurans is composed of 149 amino-acid residues with a molecular mass of 16 836 Da. ArgR was crystallized at 296 K using 1,2-propanediol as a precipitant. Crystals of N-terminally His-tagged ArgR were obtained by the sitting-drop vapour-diffusion method. Dehydrated crystals showed a dramatic improvement in diffraction qu...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Kang, J.Park, Y.W.Yeo, H.K.Lee, J.Y. Tags: ArgR transcriptional regulator dehydration research communications Source Type: research

Structures of Escherichia coli tryptophanase in holo and `semi-holo' forms
Two crystal forms of Escherichia coli tryptophanase (tryptophan indole-lyase, Trpase) were obtained under the same crystallization conditions. Both forms belonged to the same space group P43212 but had slightly different unit-cell parameters. The holo crystal form, with pyridoxal phosphate (PLP) bound to Lys270 of both polypeptide chains in the asymmetric unit, diffracted to 2.9 Å resolution. The second crystal form diffracted to 3.2 Å resolution. Of the two subunits in the asymmetric unit, one was found in the holo form, while the other appeared to be in the apo form in a wide-open conformation with two su...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Kogan, A.Raznov, L.Gdalevsky, G.Y.Cohen-Luria, R.Almog, O.Parola, A.H.Goldgur, Y. Tags: tryptophanase Escherichia coli polymorphism research communications Source Type: research

Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis
The crystal structure of the aminopeptidase APDkam589 from the thermophilic crenarchaeon Desulfurococcus kamchatkensis was determined at a resolution of 3.0 Å. In the crystal, the monomer of APDkam589 and its symmetry-related monomers are densely packed to form a 12-subunit complex. Single-particle electron-microscopy analysis confirms that APDkam589 is present as a compact dodecamer in solution. The APDkam589 molecule is built similarly to the molecules of the PhTET peptidases, which have the highest sequence identity to APDkam589 among known structures and were isolated from the more thermostable archaeon Pyrococ...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Petrova, T.E.Slutskaya, E.S.Boyko, K.M.Sokolova, O.S.Rakitina, T.V.Korzhenevskiy, D.A.Gorbacheva, M.A.Bezsudnova, E.Y.Popov, V.O. Tags: aminopeptidase APDkam598 Desulfurococcus kamchatkensis thermostability research communications Source Type: research

Purification, crystallization and preliminary X-ray diffraction studies of the β-catenin homolog HMP-2 from Caenorhabditis elegans
β-Catenin is a multifunctional protein involved in both cell adhesion and Wnt signaling in metazoans. The nematode Caenorhabditis elegans is unusual in that it expresses four β-catenin paralogs with separate functions. C. elegans HMP-2 participates in cell adhesion but not in Wnt signaling, so structural and biochemical studies of this protein will help in understanding its unusual specialization and the evolution of β-catenin. HMP-2 was expressed, purified and crystallized in two different salt conditions. Crystals grown from a sodium formate condition diffracted to a resolution of 2 Å and belonged ...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Choi, H.-J.Weis, W.I. Tags: β -catenin HMP-2 cell adhesion Caenorhabditis elegans research communications Source Type: research

Production, crystallization and X-ray diffraction analysis of a complex between a fragment of the TssM T6SS protein and a camelid nanobody
The type VI secretion system (T6SS) is a machine evolved by Gram-negative bacteria to deliver toxin effectors into target bacterial or eukaryotic cells. The T6SS is functionally and structurally similar to the contractile tail of the Myoviridae family of bacteriophages and can be viewed as a syringe anchored to the bacterial membrane by a transenvelope complex. The membrane complex is composed of three proteins: the TssM and TssL inner membrane components and the TssJ outer membrane lipoprotein. The TssM protein is central as it interacts with both TssL and TssJ, therefore linking the membranes. Using controlled trypsinoly...
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Nguyen, V.S.Spinelli, S.Desmyter, A.Le, T.T.H.Kellenberger, C.Cascales, E.Cambillau, C.Roussel, A. Tags: type VI secretion system TssM nb25 research communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of human myotubularin-related protein 1
In this study, human MTMR1 was overexpressed in Escherichia coli, purified and crystallized at 277 K using polyethylene glycol 20 000 as a precipitant. Diffraction data were collected to 2.0 Å resolution using synchrotron radiation. The crystals belonged to space group P1, with unit-cell parameters a = 67.219, b = 96.587, c = 97.581 Å, α = 87.597, β = 86.072, γ = 77.327°. Assuming the presence of four molecules in the asymmetric unit, the calculated Matthews coefficient value was 2.61 Å3 Da−1 and the corresponding solvent content was 52.9%. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2015 Category: Biochemistry Authors: Bong, S.M.Yang, S.W.Choi, J.-W.Kim, S.J.Lee, B.I. Tags: myotubularin MTMR phosphatidylinositol phosphatase research communications Source Type: research

Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of Haemophilus influenzae BamD and BamCD complex
In this study, the recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of H. influenzae BamD and BamCD complex are reported. The genes encoding BamC and BamD were cloned into a pET vector and expressed in E. coli. Affinity, ion-exchange and gel-filtration chromatography were used to obtain high-purity protein for further crystallographic characterization. Using the hanging-drop vapour-diffusion technique, BamD and BamCD protein crystals of suitable size were obtained using protein concentrations of 70 and 50 mg ml−1, respectively. Preliminary X-ray diffraction analysis...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Lei, J.Cai, X.Ma, X.Zhang, L.Li, Y.Dong, X.St Geme III, J.Meng, G. Tags: Haemophilus influenzae BamD BamCD complex research communications Source Type: research

Purification, crystallization and preliminary X-ray diffraction analysis of a soluble variant of the monoglyceride lipase Yju3p from the yeast Saccharomyces cerevisiae
The protein Yju3p is the orthologue of monoglyceride lipases in the yeast Saccharomyces cerevisiae. A soluble variant of this lipase termed s-Yju3p (38.3 kDa) was generated and purified to homogeneity by affinity and size-exclusion chromatography. s-Yju3p was crystallized in a vapour-diffusion setup at 293 K and a complete data set was collected to 2.4 Å resolution. The crystal form was orthorhombic (space group P212121), with unit-cell parameters a = 77.2, b = 108.6, c = 167.7 Å. The asymmetric unit contained four molecules with a solvent content of 46.4%. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Rengachari, S.Aschauer, P.Sturm, C.Oberer, M. Tags: s-Yju3p monoacylglycerol lipase monoglyceride lipase research communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of a putative carbon–carbon bond hydrolase from Mycobacterium abscessus 103
The PhlG protein from Mycobacterium abscessus 103 (mPhlG), which shares 30% sequence identity with phloretin hydrolase from Eubacterium ramulus and 38% sequence identity with 2,4-diacetylphloroglucinol hydrolase from Pseudomonas fluorescens Pf-5, is a putative carbon–carbon bond hydrolase. Here, the expression, purification and crystallization of mPhlG are reported. Crystals were obtained using a precipitant consisting of 100 mM citric acid pH 5.0, 1.0 M lithium chloride, 8%(w/v) polyethylene glycol 6000. The crystals diffracted to 1.87 Å resolution and belonged to space group P21, with unit-cell paramete...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Zhang, Z.Jiang, Y.-L.Wu, Y.He, Y.-X. Tags: PhlG carbon – carbon bond hydrolase Mycobacterium abscessus 103 research communications Source Type: research

Crystallization of two operator complexes from the Vibrio cholerae HigBA2 toxin–antitoxin module
The HigA2 antitoxin and the HigBA2 toxin–antitoxin complex from Vibrio cholerae were crystallized in complex with their operator box. Screening of 22 different DNA duplexes led to two crystal forms of HigA2 complexes and one crystal form of a HigBA2 complex. Crystals of HigA2 in complex with a 17 bp DNA duplex belong to space group P3221, with unit-cell parameters a = b = 94.0, c = 123.7 Å, and diffract to 2.3 Å resolution. The second form corresponding to HigA2 in complex with a 19 bp duplex belong to space group P43212 and only diffract to 3.45 Å resolution. Crystals of the HigBA2 toxin&...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Hadži, S.Garcia-Pino, A.Gerdes, K.Lah, J.Loris, R. Tags: persistence toxin – antitoxin module protein DNA complex macromolecular complex research communications Source Type: research

Purification, identification and preliminary crystallographic studies of an allergenic protein from Solanum melongena
Solanum melongena (eggplant), a member of the Solanaceae family, is a widely cultivated vegetable crop and is commonly used as a food throughout the world. Allergic reactions caused by members of this family are well known. However, mechanistic analyses to understand their molecular basis have not been adequately explored. In order to address this issue, the 7S vicilin protein (SM80.1) of size 45 kDa was purified from seeds of S. melongena by ammonium sulfate fractionation and size-exclusion chromatography. Significant homology of SM80.1 to an allergy-related protein from S. lycopersicum was identified through a BLAST se...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Jain, A.Salunke, D.M. Tags: Solanaceae Solanum melongena allergy research communications Source Type: research

Crystallization and preliminary X-ray diffraction studies of the family 54 carbohydrate-binding module from laminarinase (β-1,3-glucanase) Lic16A of Clostridium thermocellum
The crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding module (CBM) from laminarinase Lic16A of the hyperthermophilic anaerobic bacterium Clostridium thermocellum (ctCBM54) are reported. Recombinant ctCBM54 was prepared using an Escherichia coli/pQE30 overexpression system and was crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.1 Å resolution using synchrotron radiation. The crystals belonged to space group P6322, with unit-cell parameters a = b = 130.15, c = 131.05 Å. The three-dimensional structure of ctCBM54 will pro...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Kislitsyn, Y.A.Samygina, V.R.Dvortsov, I.A.Lunina, N.A.Kuranova, I.P.Velikodvorskaya, G.A. Tags: carbohydrate-binding module β -1,3-glucanase Clostridium thermocellum Lic16A research communications Source Type: research

Cloning, refolding, purification and preliminary crystallographic analysis of the sensory domain of the Campylobacter chemoreceptor for multiple ligands (CcmL)
A periplasmic sensory domain of the Campylobacter jejuni chemoreceptor for multiple ligands (CcmL) has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 as a precipitating agent. A complete data set was collected to 1.3 Å resolution using cryocooling conditions and synchrotron radiation. The crystals belonged to space group P21, with unit-cell parameters a = 42.6, b = 138.0, c = 49.0 Å, β = 94.3°. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Machuca, M.A.Liu, Y.C.Beckham, S.A.Roujeinikova, A. Tags: Campylobacter jejuni chemotaxis transducer-like proteins methyl-accepting proteins research communications Source Type: research

Crystallization and preliminary X-ray crystallographic studies of dipeptidyl peptidase 11 from Porphyromonas gingivalis
Dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) preferentially cleaves substrate peptides with Asp and Glu at the P1 position [NH2–P2–P1(Asp/Glu)–P1′–P2′…]. For crystallographic studies, PgDPP11 was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data to 1.82 Å resolution were collected from an orthorhombic crystal form belonging to space group C2221, with unit-cell parameters a = 99.33, b = 103.60, c = 177.33 Å. Structural analysis by the multi-wavelength anomalous diffra...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Sakamoto, Y.Suzuki, Y.Iizuka, I.Tateoka, C.Roppongi, S.Fujimoto, M.Gouda, H.Nonaka, T.Ogasawara, W.Tanaka, N. Tags: dipeptidyl peptidase DPP11 Porphyromonas gingivalis research communications Source Type: research

Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate
4-Nitrophenyl phosphate (p-nitrophenyl phosphate, pNPP) is widely used as a small molecule phosphotyrosine-like substrate in activity assays for protein tyrosine phosphatases. It is a colorless substrate that upon hydrolysis is converted to a yellow 4-nitrophenolate ion that can be monitored by absorbance at 405 nm. Therefore, the pNPP assay has been widely adopted as a quick and simple method to assess phosphatase activity and is also commonly used in assays to screen for inhibitors. Here, the first crystal structure is presented of a dual-specificity phosphatase, human dual-specificity phosphatase 22 (DUSP22), in compl...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Lountos, G.T.Cherry, S.Tropea, J.E.Waugh, D.S. Tags: dual-specificity phosphatase 22 4-nitrophenyl phosphate research communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of Z-ring-associated protein (ZapD) from Escherichia coli
Bacterial cytokinesis is accomplished by the Z-ring, which is a polymeric structure that includes the tubulin homologue FtsZ at the division site. ZapD, a Z-ring-associated protein, directly binds to FtsZ and stabilizes the polymerization of FtsZ to form a stable Z-ring during cytokinesis. Structural analysis of ZapD from Escherichia coli was performed to investigate the mechanism of ZapD-mediated FtsZ stabilization and polymerization. ZapD was crystallized using a reservoir solution consisting of 1.5 M lithium sulfate, 0.1 M HEPES pH 7.8, 2%(v/v) polyethylene glycol 400. X-ray diffraction data were collected to 2.95...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Son, S.H.Lee, H.H. Tags: bacterial cytokinesis FtsZ ZapD research communications Source Type: research

Crystallization and preliminary crystallographic analysis of the putative sugar-binding protein Msmeg_0515 (AgaE) from Mycobacterium smegmatis
Msmeg_0515, a gene from Mycobacterium smegmatis strain 155 encoding the ligand-binding domain, AgaE, of a putative ABC sugar transporter system, has been cloned into a pET-28a vector system, overexpressed in Escherichia coli and purified. The truncated protein lacking the first 27 residues, which correspond to a N-terminal signal sequence, was crystallized using the sitting-drop vapour-diffusion technique. The crystals of this protein diffracted to 1.48 Å resolution and belonged to space group P212121, with unit-cell parameters a = 64.06, b = 69.26, c = 100.74 Å, α = β = γ = 90° and wit...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Almourfi, F.M.Rodgers, H.F.Sedelnikova, S.E.Baker, P.J. Tags: Msmeg_0515 AgaE Mycobacterium smegmatis research communications Source Type: research

Preliminary X-ray crystallographic analysis of an engineered variant of human chimera-type galectin-3 with a shortened N-terminal domain
How lectins translate sugar-encoded information into cellular effects not only depends on glycan recognition. Other domains of the protein can contribute to the functional profile of a lectin. Human galectin-3 (Gal-3), an adhesion/growth-regulatory galectin, is composed of three different domains and is thus called a chimera-type protein. In addition to the carbohydrate-recognition domain, this lectin encompasses an N-terminal domain consisting of a peptide harbouring two phosphorylation sites and nine non-triple-helical collagen-like repeats. This region plays an as yet structurally undefined role in Gal-3 aggregation and...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Flores-Ibarra, A.Ruiz, F.M.Vértesy, S.André, S.Gabius, H.-J.Romero, A. Tags: collagen galectin-3 glycome lipopolysaccharide research communications Source Type: research

Structural basis for the recognition of the scaffold protein Frmpd4/Preso1 by the TPR domain of the adaptor protein LGN
The adaptor protein LGN interacts via the N-terminal domain comprising eight tetratricopeptide-repeat (TPR) motifs with its partner proteins mInsc, NuMA, Frmpd1 and Frmpd4 in a mutually exclusive manner. Here, the crystal structure of the LGN TPR domain in complex with human Frmpd4 is described at 1.5 Å resolution. In the complex, the LGN-binding region of Frmpd4 (amino-acid residues 990–1011) adopts an extended structure that runs antiparallel to LGN along the concave surface of the superhelix formed by the TPR motifs. Comparison with the previously determined structures of the LGN–Frmpd1, LGN–mI...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Takayanagi, H.Yuzawa, S.Sumimoto, H. Tags: LGN Frmpd4 research communications Source Type: research

Expression, purification, crystallization and preliminary X-ray diffraction analysis of the effector-interaction domain of the resistance protein RGA5-A from Oryza sativa L. japonica
RGA5-A, a component of the Pia resistance-protein complex (RGA4/RGA5-A) from Oryza sativa L. japonica, has the ability to interact physically with the effector protein AVR-Pia from Magnaporthe oryzae via its effector-interaction domain RGA5-A_S. The interaction between RGA5-A and AVR-Pia relieves the repression of RGA4, leading to AVR-independent cell death by the freed RGA4. To further understand the details of this interaction, the effector-interaction domain RGA5-A_S was expressed in Escherichia coli and purified to homogeneity. The purified recombinant protein His-RGA5-A_S was successfully crystallized using the sittin...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Huang, D.Zhang, Y.Zhao, Y.Liu, J.Peng, Y.-L. Tags: Oryza sativa L. japonica resistance protein RGA5-A research communications Source Type: research

Structural analysis of ibuprofen binding to human adipocyte fatty-acid binding protein (FABP4)
Inhibition of human adipocyte fatty-acid binding protein (FABP4) has been proposed as a treatment for type 2 diabetes, fatty liver disease and atherosclerosis. However, FABP4 displays a naturally low selectivity towards hydrophobic ligands, leading to the possibility of side effects arising from cross-inhibition of other FABP isoforms. In a search for structural determinants of ligand-binding selectivity, the binding of FABP4 towards a group of small molecules structurally related to the nonsteroidal anti-inflammatory drug ibuprofen was analyzed through X-ray crystallography. Several specific hydrophobic interactions are s...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: González, J.M.Fisher, S.Z. Tags: human fatty-acid binding protein adipocyte aP2 ALBP iLBP FABP4 ibuprofen research communications Source Type: research

The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis
Proteins are dynamic systems and interact with their environment. The analysis of crystal contacts in the most accurately determined protein structures (d
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Devedjiev, Y.D. Tags: protein crystallization static disorder conformational entropy surface mutagenesis molecular shape research communications Source Type: research

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of tomato β-galactosidase 4
Plant β-galactosidases play important roles in carbohydrate-reserve mobilization, cell-wall expansion and degradation, and turnover of signalling molecules during ripening. Tomato β-galactosidase 4 (TBG4) not only has β-galactosidase activity but also has exo-β-(1,4)-galactanase activity, and prefers β-(1,4)-galactans longer than pentamers as its substrates; most other β-galactosidases only have the former activity. Recombinant TBG4 protein expressed in the yeast Pichia pastoris was crystallized by the sitting-drop vapour-diffusion method using PEG 10 000 as a precipitant. The crystals belon...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Eda, M.Ishimaru, M.Tada, T. Tags: β -galactosidase Solanum lycopersicum plant cell wall TBG4 research communications Source Type: research

Expression, crystallization and preliminary crystallographic data analysis of VioD, a hydroxylase in the violacein-biosynthesis pathway
Violacein, a natural purple secondary metabolite, is sequentially biosynthesized by five enzymes in the following pathway: VioA–VioB–VioE–VioD–VioC. VioD, a flavin-dependent oxygenase, catalyzes the hydroxylation of the intermediate product prodeoxyviolaceinic acid (PVA) at the 5-position of one indole ring to yield proviolacein. In vitro biochemical data have revealed this process, but the catalytic mechanism still remains largely unclear. Here, the cloning, expression, purification, crystallization and diffraction of VioD are reported. Crystals of VioD diffracted to 1.7 Å resolution and be...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Ran, T.Gao, M.Wei, Q.He, J.Tang, L.Wang, W.Xu, D. Tags: violacein VioD research communications Source Type: research

Structure of the apo anti-influenza CH65 Fab
Influenza viruses remain a persistent challenge to human health owing to their inherent ability to evade the immune response by antigenic drift. However, the discovery of broadly neutralizing antibodies (bnAbs) against divergent viruses has sparked renewed interest in a universal influenza vaccine and novel therapeutic opportunities. Here, a crystal structure at 1.70 Å resolution is presented of the Fab of the human antibody CH65, which has broad neutralizing activity against a range of seasonal H1 isolates. Previous studies proposed that affinity maturation of this antibody lineage pre-organizes the complementarit...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Lee, P.S.Arnell, A.J.Wilson, I.A. Tags: influenza antibody adaptive immunity affinity maturation research communications Source Type: research

Expression, purification and preliminary crystallographic analysis of a haem-utilizing protein, HutX, from Vibrio cholerae
Vibrio cholerae, the causative agent of cholera, has developed a variety of mechanisms to obtain the limited-availability iron from human hosts. One important method for iron acquisition is through haem-uptake systems. Although the transport of haem has been widely studied, the fate of haem once it enters the cytoplasm remains an open question. Here, preliminary X-ray crystallographic analysis was performed on HutX, a member of the conserved haem-utilization operon from V. cholerae strain N16961. The crystals of HutX were found to belong to the orthorhombic space group C2221, with unit-cell parameters a = 50.1, b = 169.0, ...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Su, T.Chi, K.Wang, K.Guo, L.Huang, Y. Tags: haem uptake iron acquisition Vibrio cholerae research communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of Paenibacillus barcinonensis xylanase 10C containing the CBM22-1–CBM22-2 tandem
This study represents the first structure containing two contiguous CBM22 modules, which will contribute to a better understanding of the role that this multiplicity plays in fine-tuning substrate affinity. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Sainz-Polo, M.Á.González, B.Pastor, F.I.J.Sanz-Aparicio, J. Tags: carbohydrate-binding domain CBM22 Paenibacillus bacterial xylanase xylan-binding domain research communications Source Type: research

Preliminary X-ray analysis of the binding domain of the soybean vacuolar sorting receptor complexed with a sorting determinant of a seed storage protein
β-Conglycinin is a major seed storage protein in soybeans, which are an important source of protein. The major subunits (α, α′ and β) of β-conglycinin are sorted to protein-storage vacuoles in seed cells. Vacuolar sorting receptor (VSR) is an integral membrane protein that recognizes the sorting determinant of vacuolar proteins, including β-conglycinin, and regulates their sorting process. Vacuolar sorting determinants of the α′ and β subunits of β-conglycinin exist in their C-terminal peptides. Here, the preliminary X-ray diffraction analysis of the binding domai...
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Maruyama, N.Goshi, T.Sugiyama, S.Niiyama, M.Adachi, H.Takano, K.Murakami, S.Inoue, T.Mori, Y.Matsumura, H.Mikami, B. Tags: soybean seed storage protein β -conglycinin vacuolar sorting receptor research communications Source Type: research

Latest methods of fluorescence-based protein crystal identification
Successful protein crystallization screening experiments are dependent upon the experimenter being able to identify positive outcomes. The introduction of fluorescence techniques has brought a powerful and versatile tool to the aid of the crystal grower. Trace fluorescent labeling, in which a fluorescent probe is covalently bound to a subpopulation ( (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - January 28, 2015 Category: Biochemistry Authors: Meyer, A.Betzel, C.Pusey, M. Tags: protein crystal identification fluorescence research communications Source Type: research

The three-dimensional structure of the cellobiohydrolase Cel7A from Aspergillus fumigatus at 1.5 Å resolution
The enzymatic degradation of plant cell-wall cellulose is central to many industrial processes, including second-generation biofuel production. Key players in this deconstruction are the fungal cellobiohydrolases (CBHs), notably those from family GH7 of the carbohydrate-active enzymes (CAZY) database, which are generally known as CBHI enzymes. Here, three-dimensional structures are reported of the Aspergillus fumigatus CBHI Cel7A solved in uncomplexed and disaccharide-bound forms at resolutions of 1.8 and 1.5 Å, respectively. The product complex with a disaccharide in the +1 and +2 subsites adds to the growing thre...
Source: Acta Crystallographica Section F - December 24, 2014 Category: Biochemistry Authors: Moroz, O.V.Maranta, M.Shaghasi, T.Harris, P.V.Wilson, K.S.Davies, G.J. Tags: cellulase biofuels carbohydrate-active enzyme thermal stability research communications Source Type: research

Cloning, expression, refolding, purification and preliminary crystallographic analysis of the sensory domain of the Campylobacter chemoreceptor for aspartate A (CcaA)
In this study, the sensory domain of the C. jejuni chemoreceptor for aspartate A (CcaA) has been expressed in Escherichia coli and purified from inclusion bodies. The urea-denatured protein was refolded and then crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as a precipitating agent. A complete data set has been collected to 1.4 Å resolution using cryocooling conditions and synchrotron radiation. The crystals belonged to space group P1, with unit-cell parameters a = 39.3, b = 43.3, c = 50.9 Å, α = 92.5, β = 111.4, γ = 114.7°. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - December 24, 2014 Category: Biochemistry Authors: Machuca, M.A.Liu, Y.C.Roujeinikova, A. Tags: Campylobacter jejuni chemotaxis transducer-like proteins methyl-accepting proteins research communications Source Type: research