Crystallization and preliminary X-ray characterization of the dephospho-CoA kinase from Legionella pneumophila
Dephospho-CoA kinases (DPCKs) are members of the kinase family that catalyze the final step in CoA biosynthesis. Their function is phosphorylation of the 3-hydroxyl group of the ribose using ATP as a phosphate donor. Structural changes induced by ATP binding play an important role during the DPCK catalytic cycle. In this work, DPCK from Legionella pneumophila was overexpressed in Escherichia coli. The purification, crystallization and preliminary X-ray analysis of crystals of this protein are described. The protein was crystallized in space group P21212, with unit-cell parameters a = 36.29, b = 82.20, c = 81.80 Å, ...
Source: Acta Crystallographica Section F - April 15, 2014 Category: Biochemistry Authors: Yu, D.Chen, X.Xu, Z.Ge, H. Tags: dephospho-CoA kinase Legionella pneumophila crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of the XoGroEL chaperonin from Xanthomonas oryzae pv. oryzae
Along with the co-chaperonin GroES, the chaperonin GroEL plays an essential role in enhancing protein folding or refolding and in protecting proteins against misfolding and aggregation in the cellular environment. The XoGroEL gene (XOO_4288) from Xanthomonas oryzae pv. oryzae was cloned and the protein was expressed, purified and crystallized. The purified XoGroEL protein was crystallized using the hanging-drop vapour-diffusion method and a crystal diffracted to a resolution of 3.4 Å. The crystal belonged to the orthorhombic space group P212121 with 14 monomers in the asymmetric unit, with a corresponding VM of 2.7...
Source: Acta Crystallographica Section F - April 15, 2014 Category: Biochemistry Authors: Tran, H.-T.Pham, T.-V.Ngo, H.-P.-T.Hong, M.-K.Kim, J.-G.Lee, S. H.Ahn, Y.-J.Kang, L.-W. Tags: GroEL chaperone Xanthomonas oryzae pv. oryzae (Xoo) crystallization communications Source Type: research

Cloning, expression, crystallization and preliminary X-ray diffraction studies of staphylococcal superantigen-like protein 1 (SSL1)
Staphylococcus aureus produces a family of exotoxins which are structural homologues of superantigens and thus are called staphylococcal superantigen-like proteins (SSLs). Amongst the 14 SSL genes, ssl1 (SAOUHSC_00383) has been cloned in the pQE30 expression vector, overexpressed in Escherichia coli M15 (pREP4) cells and the protein purified to homogeneity. The protein was crystallized using 6% Tacsimate pH 6.0, 0.1 M MES pH 6.0, 25%(w/v) polyethylene glycol 3350, 100 mM NDSB 256 at 298 K by the sitting-drop vapour-diffusion method. The crystals belonged to space group P21, with unit-cell parameters a = 77.9, b = 70....
Source: Acta Crystallographica Section F - April 15, 2014 Category: Biochemistry Authors: Dutta, D.Dutta, A.Bhattacharjee, A.Basak, A.Das, A.K. Tags: Staphylococcus aureus superantigen-like proteins SSL1 crystallization communications Source Type: research

Expression, purification, crystallization and preliminary crystallographic study of the cytoplasmic domain of the mitochondrial dynamics protein MiD51
In this study, the cytoplasmic domain of MiD51 was overexpressed in Escherichia coli, purified and crystallized. An X-ray diffraction data set was collected to a resolution of 3.1 Å and the crystal belonged to space group P41212, with unit-cell parameters a = b = 90.1, c = 124.7 Å, α = β = γ = 90°. The asymmetric unit had the highest probability of containing one molecule, with a Matthews coefficient of 3.32 Å3 Da−1 and a solvent content of 63.0%. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - April 15, 2014 Category: Biochemistry Authors: Ma, J.Sun, F. Tags: mitochondrial dynamics mitochondrial fission mitochondrial dynamics protein MiD51 crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of the cardiac transcription factor complex of NKX2.5 and TBX5 with DNA
Heart development depends on timely expression of genes regulated by combinatorial interactions of master cardiac transcription factors. To elucidate the molecular basis of their interactions, a ternary complex of cardiac transcription factors, NKX2.5 and TBX5, and their target DNA was studied using X-ray crystallography. Here, the purification, crystallization and preliminary X-ray crystallographic analyses of the NKX2.5 homeodomain and TBX5 DNA-binding domain complex with a DNA element from the −252 promoter region of the atrial natriuretic factor are reported. The crystal diffracted to 2.88 Å resolution an...
Source: Acta Crystallographica Section F - April 15, 2014 Category: Biochemistry Authors: Pradhan, L.Gopal, S.Nam, H.-J. Tags: NKX2.5 TBX5 target DNA cardiac transcription factors crystallization communications Source Type: research

Purification, crystallization and preliminary crystallographic analysis of a ribosome-recycling factor from Thermoanaerobacter tengcongensis (TteRRF)
Ribosome-recycling factor (RRF) plays an essential role in the fourth step of protein synthesis in prokaryotes. RRF combined with elongation factor G (EF-G) disassembles the post-termination ribosome complex and recycles the protein synthesis machine for the next round of translation. A reductive-methylation-modified RRF from Thermoanaerobacter tengcongensis (TteRRF) has been crystallized using the vapour-diffusion method. The crystal grew in a condition consisting of 0.1 M citric acid pH 3.5, 3.0 M NaCl and 50 mg ml−1 methylated protein solution at 289 K. A complete data set was collected from a crystal to...
Source: Acta Crystallographica Section F - April 15, 2014 Category: Biochemistry Authors: Shang, G.Feng, D.Lu, F.Zhang, H.Cang, H.Gao, W.Bi, R. Tags: ribosome-recycling factor Thermoanaerobacter tengcongensis crystallization communications Source Type: research

Structure of catabolite activator protein with cobalt(II) and sulfate
The crystal structure of cyclic AMP–catabolite activator protein (CAP) from Escherichia coli containing cobalt(II) chloride and ammonium sulfate is reported at 1.97 Å resolution. Each of the two CAP subunits in the asymmetric unit binds one cobalt(II) ion, in each case coordinated by N-terminal domain residues His19, His21 and Glu96 plus an additional acidic residue contributed via a crystal contact. The three identified N-terminal domain cobalt-binding residues are part of a region of CAP that is important for transcription activation at class II CAP-dependent promoters. Sulfate anions mediate additional cry...
Source: Acta Crystallographica Section F - April 15, 2014 Category: Biochemistry Authors: Rao, R.R.Lawson, C.L. Tags: catabolite activator protein Escherichia coli structural communications Source Type: research

Structure of the Arabidopsis thaliana TOP2 oligopeptidase
Thimet oligopeptidase (TOP) is a zinc-dependent metallopeptidase. Recent studies suggest that Arabidopsis thaliana TOP1 and TOP2 are targets for salicylic acid (SA) binding and participate in SA-mediated plant innate immunity. The crystal structure of A. thaliana TOP2 has been determined at 3.0 Å resolution. Comparisons to the structure of human TOP revealed good overall structural conservation, especially in the active-site region, despite their weak sequence conservation. The protein sample was incubated with the photo-activated SA analog 4-azido-SA and exposed to UV irradiation before crystallization. However, t...
Source: Acta Crystallographica Section F - April 14, 2014 Category: Biochemistry Authors: Wang, R.Rajagopalan, K.Sadre-Bazzaz, K.Moreau, M.Klessig, D.F.Tong, L. Tags: Arabidopsis thaliana thimet oligopeptidase (TOP) structural communications Source Type: research

Notes for authors
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 31, 2014 Category: Biochemistry Authors: IUCr Editorial Office Tags: Notes for authors international union of crystallography Source Type: research

Mechanisms, kinetics, impurities and defects: consequences in macromolecular crystallization
The nucleation and growth of protein, nucleic acid and virus crystals from solution are functions of underlying kinetic and thermodynamic parameters that govern the process, and these are all supersaturation-dependent. While the mechanisms of macromolecular crystal growth are essentially the same as for conventional crystals, the underlying parameters are vastly different, in some cases orders of magnitude lower, and this produces very different crystallization processes. Numerous physical features of macromolecular crystals are of serious interest to X-ray diffractionists; the resolution limit and mosaicity, for example, ...
Source: Acta Crystallographica Section F - March 28, 2014 Category: Biochemistry Authors: McPherson, A.Kuznetsov, Y.G. Tags: atomic force microscopy crystal growth protein crystals virus crystals nucleation X-ray diffraction solution growth crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of PBPD2 from Listeria monocytogenes
In this study, PBPD2, a low-molecular-weight PBP encoded by lmo2812 from Listeria monocytogenes, was overexpressed in Escherichia coli, purified and crystallized at 295 K using the sitting-drop vapour-diffusion method. The crystal belonged to the primitive orthorhombic space group P212121, with unit-cell parameters a = 37.7, b = 74.7, c = 75.1 Å, and diffracted to 1.55 Å resolution. There was one molecule in the asymmetric unit. The preliminary structure was determined by the molecular-replacement method. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Cha, H.J.Jeong, J.-H.Kim, Y.-G. Tags: penicillin-binding proteins PBPD2 Listeria monocytogenes crystallization communications Source Type: research

Frq2 from Drosophila melanogaster: cloning, expression, purification, crystallization and preliminary X-ray analysis
Drosophila melanogaster contains two calcium-binding proteins, Frq1 and Frq2, in the nervous system that control the number of synapses and the probability of release. To understand the differential function of the two proteins, whose sequence is only 5% dissimilar, the crystal structures of Frq1 and Frq2 are needed. Here, the cloning, expression, purification, crystallization and preliminary crystallographic analysis of Frq2 are presented. The full-length protein was purified using a two-step chromatographic procedure. Two different diffracting crystal forms were obtained using a progressive streak-seeding method and dete...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Baños-Mateos, S.Chaves-Sanjuán, A.Mansilla, A.Ferrús, A.Sánchez-Barrena, M.J. Tags: calcium-binding proteins Drosophila melanogaster Frq2 crystallization communications Source Type: research

Successful data recovery from oscillation photographs containing strong polycrystalline diffraction rings from an unknown small-molecule contaminant: preliminary structure solution of Salmonella typhimurium pyridoxal kinase (PdxK)
Pyridoxal kinase (PdxK; EC 2.7.1.35) belongs to the phosphotransferase family of enzymes and catalyzes the conversion of the three active forms of vitamin B6, pyridoxine, pyridoxal and pyridoxamine, to their phosphorylated forms and thereby plays a key role in pyridoxal 5′-phosphate salvage. In the present study, pyridoxal kinase from Salmonella typhimurium was cloned and overexpressed in Escherichia coli, purified using Ni–NTA affinity chromatography and crystallized. X-ray diffraction data were collected to 2.6 Å resolution at 100 K. The crystal belonged to the primitive orthorhombic space group P21...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Deka, G.Kalyani, J.N.Benazir, J.F.Savithri, H.S.Murthy, M.R.N. Tags: pyridoxal kinase Salmonella typhimurium crystallization communications Source Type: research

Crystallization and preliminary crystallographic analysis of manganese lipoxygenase
Lipoxygenases constitute a family of nonhaem metal enzymes with catalytic iron or, occasionally, catalytic manganese. Lipoxygenases oxidize polyunsaturated fatty acids with position specificity and stereospecificity to hydroperoxides, which contribute to inflammation and the development of cancer. Little is known about the structural differences between lipoxygenases with Fe or Mn and the metal-selection mechanism. A Pichia pastoris expression system was used for the production of the manganese lipoxygenase of the take-all fungus of wheat, Gaeumannomyces graminis. The active enzyme was treated with α-mannosidase, pur...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Wennman, A.Oliw, E.H.Karkehabadi, S. Tags: manganese lipoxygenase Gaeumannomyces graminis crystallization communications Source Type: research

Recombinant production, purification and crystallization of the Toxoplasma gondii coronin WD40 domain
Toxoplasma gondii is one of the most widely spread parasitic organisms in the world. Together with other apicomplexan parasites, it utilizes a special actin–myosin motor for its cellular movement, called gliding motility. This actin-based process is regulated by a small set of actin-binding proteins, which in Apicomplexa comprises only 10–15 proteins, compared with>150 in higher eukaryotes. Coronin is a highly conserved regulator of the actin cytoskeleton, but its functions, especially in parasites, have remained enigmatic. Coronins consist of an N-terminal actin-binding β-propeller WD40 domain, followe...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Kallio, J.P.Kursula, I. Tags: coronin WD40 domain actin-binding protein Toxoplasma apicomplexan parasite crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic studies of transglutaminase 2 in complex with Ca2+
Transglutaminase 2 (TG2) is a multi-functional protein that has been implicated in a variety of physiological cellular activities, including apoptosis, angiogenesis and cellular differentiation. Two functions of TG2 are protein cross-linking and GTP hydrolysis activities. The protein cross-linking activity of TG2 is positively controlled by calcium; however, the molecular mechanism of its Ca2+-dependent activity is completely unknown. In the present study, full-length human TG2 in complex with Ca2+ was overexpressed, purified and crystallized at 20°C as a first step towards elucidating this mechanism. X-ray diffraction...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Jang, T.-H.Park, H.H. Tags: transglutaminase 2 protein cross-linking crystallization communications Source Type: research

Preliminary crystallographic analysis of the ankyrin-repeat domain of Arabidopsis thaliana AKT1: identification of the domain boundaries for protein crystallization
The Arabidopsis thaliana K+ transporter 1 (AKT1) participates in the maintenance of an adequate cell potassium (K+) concentration. The CBL-interacting protein kinase 23 (CIPK23) activates AKT1 for K+ uptake under low-K+ conditions. This process is mediated by the interaction between the cytosolic ankyrin-repeat (AR) domain of AKT1 and the kinase domain of CIPK23. However, the precise boundaries of the AR domain and the residues responsible for the interaction are still unknown. Here, the optimization procedure to obtain an AR domain construct suitable for crystallization and the preliminary crystallographic analysis of the...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Chaves-Sanjuán, A.Sánchez-Barrena, M.J.González-Rubio, J.M.Albert, A. Tags: AKT1 K transporter 1 Arabidopsis thaliana crystallization communications Source Type: research

Expression, crystallization and preliminary X-ray crystallographic analysis of d-alanine-d-alanine ligase from OXA-23-producing Acinetobacter baumannii K0420859
Acinetobacter baumannii causes bacteraemia, pneumonia, other respiratory-tract and urinary-tract infections in humans. OXA-23 carbapenemase-producing A. baumannii K0420859 (A. baumannii OXA-23) is resistant to carbapenem, a common antibacterial drug. To develop an efficient and novel antibacterial drug against A. baumannii OXA-23, d-alanine-d-alanine ligase, which is essential in bacterial cell-wall synthesis, is of interest. Here, the d-alanine-d-alanine ligase (AbDdl) gene from A. baumannii OXA-23 was cloned and expressed, and the AbDdl protein was purified and crystallized; this enzyme can be used as a novel target for ...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Huynh, K.H.Tran, H.-T.Pham, T.-V.Ngo, H.-P.-T.Cha, S.-S.Chung, K.M.Lee, S.H.Kang, L.-W. Tags: OXA-23-producing Acinetobacter baumannii cell-wall synthesis d-alanine-d-alanine ligase crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of importin-α from Neurospora crassa
Importin-α recognizes cargo proteins that contain classical nuclear localization sequences (NLS) and, in complex with importin-β, is able to translocate nuclear proteins through the nuclear pore complex. The filamentous fungus Neurospora crassa is a well studied organism that has been widely used as a model organism for fundamental aspects of eukaryotic biology, and is important for understanding the specific mechanisms of protein transport to the cell nucleus. In this work, the crystallization and preliminary X-ray diffraction analysis of importin-α from N. crassa (IMPα-Nc) complexed with a classica...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Bernardes, N.E.Takeda, A.A.S.Freitas, F.Z.Bertolini, M.C.Fontes, M.R.M. Tags: Neurospora crassa importin- α NLS peptide crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray diffraction analysis of ArsH from Synechocystis sp. strain PCC 6803
ArsH is an NADPH-dependent flavin mononucleotide reductase and is frequently encoded as part of an ars operon. The function of the arsH gene remains to be characterized. Crystallization and structural studies may contribute to elucidating the specific biological function of ArsH associated with arsenic resistance. ArsH from Synechocystis sp. strain PCC 6803 was overproduced, purified and crystallized. Crystals were obtained by the sitting-drop vapour-diffusion method. Diffraction data were collected and processed to a resolution of 1.6 Å. The crystals belonged to the tetragonal space group I4122, with unit-cell par...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Zhang, X.Xue, X.-M.Yan, Y.Ye, J. Tags: ArsH Synechocystis arsenic crystallization communications Source Type: research

Overexpression, crystallization and preliminary X-ray crystallographic analysis of the ectoine hydroxylase from Sphingopyxis alaskensis
The ectoine hydroxylase (EctD) is a member of the non-haem-containing iron(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. Its mononuclear iron centre is a prerequisite for the activity of this enzyme and promotes the O2-dependent oxidative decarboxylation of 2-oxoglutarate, which is coupled to a two-electron oxidation of the substrate ectoine to yield 5-hydroxyectoine. An expression and purification protocol for the EctD enzyme from Sphingopyxis alaskensis was developed and the protein was crystallized using the sitting-drop vapour-diffusion method. This resulted in two different crystal forms, representing the...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Hoeppner, A.Widderich, N.Bremer, E.Smits, S.H.J. Tags: ectoine hydroxylase Sphingopyxis alaskensis crystallization communications Source Type: research

Cloning, crystallization and preliminary X-ray diffraction analysis of an intact DNA methyltransferase of a type I restriction–modification enzyme from Vibrio vulnificus
Independently of the restriction (HsdR) subunit, the specificity (HsdS) and methylation (HsdM) subunits interact with each other, and function as a methyltransferase in type I restriction–modification systems. A single gene that combines the HsdS and HsdM subunits in Vibrio vulnificus YJ016 was expressed and purified. A crystal suitable for X-ray diffraction was obtained from 25%(w/v) polyethylene glycol monomethylether 5000, 0.1 M HEPES pH 8.0, 0.2 M ammonium sulfate at 291 K by hanging-drop vapour diffusion. Diffraction data were collected to a resolution of 2.31 Å using synchrotron radiation. The cry...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Huynh Thi Yen, L.Park, S.-Y.Kim, J.-S. Tags: type I restriction and modification specificity subunit methylation subunit DNA methyltransferases crystallization communications Source Type: research

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium butyricum
(S)-3-Hydroxybutyryl-CoA dehydrogenase from Clostridium butyricum (CbHBD) is an enzyme that catalyzes the second step in the biosynthesis of n-butanol from acetyl-CoA by the reduction of acetoacetyl-CoA to 3-hydroxybutyryl-CoA. The CbHBD protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 2 M ammonium sulfate, 0.1 M CAPS pH 10.5, 0.2 M lithium sulfate at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.3 Å on a synchrotron beamline. The crystal belonged to space group R3, with unit-cell parameters a = b = 148.5, c = 201.6 Å. With four m...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Kim, E.-J.Kim, K.-J. Tags: (S)-3-hydroxybutyryl-CoA dehydrogenase Clostridium butyricum n-butanol crystallization communications Source Type: research

Purification, crystallization and X-ray crystallographic studies on a putative methyltransferase, YtqB, from Bacillus subtilis
S-Adenosyl-l-methionine (SAM)-dependent methyltransferases (MTases) catalyze the transfer of a methyl group from a SAM cofactor to specific substrate molecules, including small chemicals, proteins, DNAs and RNAs, and are required for various cellular functions, such as regulation of gene expression and biosynthesis of metabolites. Bacillus subtilis YtqB is a putative SAM-dependent MTase whose biological function has not been characterized. To provide biochemical and structural insights into the role of YtqB in bacteria, the recombinant YtqB protein was overexpressed in the Escherichia coli expression system and purified by...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Park, S.C.Song, W.S.Wi, J.Yoon, S.I. Tags: Bacillus subtilis YtqB methyltransferases S-adenosyl-l-methionine crystallization communications Source Type: research

Preliminary crystallographic analysis of a double mutant of the acetyl xylo-oligosaccharide esterase Axe2 in its dimeric form
Xylans are polymeric sugars constituting a significant part of the plant cell wall. They are usually substituted with acetyl side groups attached at positions 2 or 3 of the xylose backbone units. Acetylxylan esterases are part of the hemicellulolytic system of many microorganisms which utilize plant biomass for growth. These enzymes hydrolyze the ester linkages of the xylan acetyl groups and thus improve the accessibility of main-chain-hydrolyzing enzymes and their ability to break down the sugar backbone units. The acetylxylan esterases are therefore critically important for those microorganisms and as such could be used ...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Lansky, S.Alalouf, O.Salama, R.Dvir, H.Shoham, Y.Shoham, G. Tags: Geobacillus stearothermophilus xylan utilization xylan esterase serine esterase double mutant oligomerization crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of a novel type of lipolytic hydrolase from Bacillus licheniformis
With increasing demand in biotechnological applications, the identification and characterization of novel lipolytic enzymes are of great importance. The crystallization and preliminary X-ray crystallographic study of a novel type of hydrolase from Bacillus licheniformis (BL28) are described here. Recombinant BL28 protein containing a C-terminal His tag was overproduced in Escherichia coli and purified to homogeneity. BL28 was crystallized using 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 30%(w/v) PEG 4000 as a crystallizing solution. X-ray diffraction data were collected to a resolution of 1...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Ju, H.Pandian, R.Kim, K.Kim, K.K.Kim, T.D. Tags: lipolytic hydrolase Bacillus licheniformis crystallization communications Source Type: research

Crystallization and preliminary neutron diffraction experiment of human farnesyl pyrophosphate synthase complexed with risedronate
Nitrogen-containing bisphosphonates (N-BPs), such as risedronate and zoledronate, are currently used as a clinical drug for bone-resorption diseases and are potent inhibitors of farnesyl pyrophosphate synthase (FPPS). X-ray crystallographic analyses of FPPS with N-BPs have revealed that N-BPs bind to FPPS with three magnesium ions and several water molecules. To understand the structural characteristics of N-BPs bound to FPPS, including H atoms and hydration by water, neutron diffraction studies were initiated using BIODIFF at the Heinz Maier-Leibnitz Zentrum (MLZ). FPPS–risedronate complex crystals of approximate di...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Yokoyama, T.Ostermann, A.Mizuguchi, M.Niimura, N.Schrader, T.E.Tanaka, I. Tags: neutron protein crystallography farnesyl pyrophosphate synthase crystallization communications Source Type: research

Expression, purification, crystallization and preliminary X-ray diffraction analysis of a mammalian type 10 adenylyl cyclase
The second messenger cAMP is synthesized in mammals by ten differently regulated adenylyl cyclases (AC1–10). These ACs are grouped into nucleotidyl cyclase class III based on homologies in their catalytic domains. The catalytic domain of AC10 is unique, however, in being activated through direct interaction with calcium and bicarbonate. Here, the production, crystallization and X-ray diffraction analysis of the catalytic domain of human AC10 are described as a basis for structural studies of regulator binding sites and mechanisms. The recombinant protein had high specific AC activity, and crystals of AC10 in space gr...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Kleinboelting, S.van den Heuvel, J.Kambach, C.Weyand, M.Leipelt, M.Steegborn, C. Tags: soluble adenylyl cyclase type 10 mammalian catalytic core crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of α-glucosidase HaG from Halomonas sp. strain H11
The α-glucosidase HaG from the halophilic bacterium Halomonas sp. strain H11 catalyzes the hydrolysis of the glucosidic linkage at the nonreducing end of α-glucosides, such as maltose and sucrose, to release α-glucose. Based on its amino-acid sequence, this enzyme is classified as a member of glycoside hydrolase family 13. HaG has three unique characteristics: (i) a very narrow substrate specificity, almost exclusively hydrolyzing disaccharides; (ii) activation by monovalent cations, such as K+, Rb+, Cs+ and NH4+; and (iii) high transfer activity of the glucose moiety to the OH group of low-molecular-weig...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Shen, X.Saburi, W.Gai, Z.-Q.Komoda, K.Yu, J.Ojima-Kato, T.Kido, Y.Matsui, H.Mori, H.Yao, M. Tags: HaG Halomonas sp. strain H11 crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of domain-chimeric l-(2S,3S)-butanediol dehydrogenase
A domain-chimeric l-2,3-butanediol dehydrogenase (chimera l-BDH), which was designed to possess both the S-configuration specificity of l-BDH and the stability of meso-BDH, was constructed by exchanging the respective domains of these two BDHs. However, chimera l-BDH possessed a lower enzymatic function than expected based on the two original enzymes. To elucidate the causes of the decreased stability and substrate specificity, crystallization of the protein was performed. Chimera l-BDH was purified to homogeneity via ammonium sulfate fractionation and three column-chromatography steps, and was crystallized using the hangi...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Shimegi, T.Ooyama, T.Ohtsuki, T.Kurisu, G.Kusunoki, M.Ui, S. Tags: l-2,3-butanediol dehydrogenase domain chimera crystallization communications Source Type: research

Structure of the Reston ebolavirus VP30 C-terminal domain
The ebolaviruses can cause severe hemorrhagic fever. Essential to the ebolavirus life cycle is the protein VP30, which serves as a transcriptional cofactor. Here, the crystal structure of the C-terminal, NP-binding domain of VP30 from Reston ebolavirus is presented. Reston VP30 and Ebola VP30 both form homodimers, but the dimeric interfaces are rotated relative to each other, suggesting subtle inherent differences or flexibility in the dimeric interface. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Clifton, M.C.Kirchdoerfer, R.N.Atkins, K.Abendroth, J.Raymond, A.Grice, R.Barnes, S.Moen, S.Lorimer, D.Edwards, T.E.Myler, P.J.Saphire, E.O. Tags: Please provide keywords structural communications Source Type: research

Structural characterization of a novel autonomous cohesin from Ruminococcus flavefaciens
Ruminococcus flavefaciens is a cellulolytic bacterium found in the rumen of herbivores and produces one of the most elaborate and variable cellulosome systems. The structure of an R. flavefaciens protein (RfCohG, ZP_06142108), representing a freestanding (non-cellulosomal) type III cohesin module, has been determined. A selenomethionine derivative with a C-terminal histidine tag was crystallized and diffraction data were measured to 2.44 Å resolution. Its structure was determined by single-wavelength anomalous dispersion, revealing eight molecules in the asymmetric unit. RfCohG exhibits the most complex among all k...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Voronov-Goldman, M.Levy-Assaraf, M.Yaniv, O.Wisserman, G.Jindou, S.Borovok, I.Bayer, E.A.Lamed, R.Shimon, L.J.W.Frolow, F. Tags: cellulosome scaffoldin cohesin-dockerin interaction cellulose degradation glycoside hydrolases structural communications Source Type: research

Structure of human nucleosome containing the testis-specific histone variant TSH2B
The human histone H2B variant TSH2B is highly expressed in testis and may function in the chromatin transition during spermatogenesis. In the present study, the crystal structure of the human testis-specific nucleosome containing TSH2B was determined at 2.8 Å resolution. A local structural difference between TSH2B and canonical H2B in nucleosomes was detected around the TSH2B-specific amino-acid residue Ser85. The TSH2B Ser85 residue does not interact with H4 in the nucleosome, but in the canonical nucleosome the H2B Asn84 residue (corresponding to the TSH2B Ser85 residue) forms water-mediated hydrogen bonds with t...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Urahama, T.Horikoshi, N.Osakabe, A.Tachiwana, H.Kurumizaka, H. Tags: TSH2B nucleosome chromatin testis structural communications Source Type: research

Structure of the kinase domain of Gilgamesh from Drosophila melanogaster
The CK1 family kinases regulate multiple cellular aspects and play important roles in Wnt/Wingless and Hedgehog signalling. The kinase domain of Drosophila Gilgamesh isoform I (Gilgamesh-I), a homologue of human CK1-γ, was purified and crystallized. Crystals of methylated Gilgamesh-I kinase domain with a D210A mutation diffracted to 2.85 Å resolution and belonged to space group P43212, with unit-cell parameters a = b = 52.025, c = 291.727 Å. The structure of Gilgamesh-I kinase domain, which was determined by molecular replacement, has conserved catalytic elements and an active conformation. Structural...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Han, N.Chen, C.Shi, Z.Cheng, D. Tags: Gilgamesh CK1 family kinases kinase domain Drosophila melanogaster structural communications Source Type: research

Comparison of four different crystal forms of the Mycobacterium tuberculosis ESX-1 secreted protein regulator EspR
The Mycobacterium tuberculosis ESX-1 secreted protein regulator (EspR, Rv3849) is the key protein that delivers bacterial proteins into the host cell during mycobacterial infection. EspR binds directly to the espACD operon and is involved in transcriptional activation. In the current study, M. tuberculosis EspR has been crystallized and its X-ray structure has been determined at 3.3 Å resolution in a P3221 crystal form. EspR forms a physiological dimer in the crystal. Each EspR monomer contains an N-terminal helix–turn–helix DNA-binding domain and a C-terminal dimerization domain. The EspR structure in ...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Gangwar, S.P.Meena, S.R.Saxena, A.K. Tags: M. tuberculosis EspR structural communications Source Type: research

Structure of 4-pyridoxolactonase from Mesorhizobium loti
4-Pyridoxolactonase from Mesorhizobium loti catalyzes the zinc-dependent lactone-ring hydrolysis of 4-pyridoxolactone (4PAL) to 4-pyridoxic acid (4PA) in vitamin B6 degradation pathway I. The crystal structures of 4-pyridoxolactonase and its complex with 5-pyridoxolactone (5PAL; the competitive inhibitor) were determined. The overall structure was an αβ/βα sandwich fold, and two zinc ions were coordinated. This strongly suggested that the enzyme belongs to subclass B3 of the class B β-lactamases. In the complex structure, the carbonyl group of 5PAL pointed away from the active site, revealing why...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Kobayashi, J.Yoshikane, Y.Yagi, T.Baba, S.Mizutani, K.Takahashi, N.Mikami, B. Tags: zinc-dependent hydrolase docking simulation catalytic mechanisms 4-pyridoxolactonase Mesorhizobium loti vitamin B6 structural communications Source Type: research

1.15 Å resolution structure of the proteasome-assembly chaperone Nas2 PDZ domain
The 26S proteasome is a 2.5 MDa protease dedicated to the degradation of ubiquitinated proteins in eukaryotes. The assembly of this complex containing 66 polypeptides is assisted by at least nine proteasome-specific chaperones. One of these, Nas2, binds to the proteasomal AAA-ATPase subunit Rpt5. The PDZ domain of Nas2 binds to the C-terminal tail of Rpt5; however, it does not require the C-terminus of Rpt5 for binding. Here, the 1.15 Å resolution structure of the PDZ domain of Nas2 is reported. This structure will provide a basis for further insights regarding the structure and function of Nas2 in proteasome ass...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Singh, C.R.Lovell, S.Mehzabeen, N.Chowdhury, W.Q.Geanes, E.S.Battaile, K.P.Roelofs, J. Tags: Nas2 chaperones proteasome PDZ domain structural communications Source Type: research

1.55 Å resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis
The crystallographic structure of the Mycobacterium tuberculosis (TB) protein Rv3902c (176 residues; molecular mass of 19.8 kDa) was determined at 1.55 Å resolution. The function of Rv3902c is unknown, although several TB genes involved in bacterial pathogenesis are expressed from the operon containing the Rv3902c gene. The unique structural fold of Rv3902c contains two domains, each consisting of antiparallel β-sheets and α-helices, creating a hand-like binding motif with a small binding pocket in the palm. Structural homology searches reveal that Rv3902c has an overall structure similar to that of th...
Source: Acta Crystallographica Section F - March 25, 2014 Category: Biochemistry Authors: Reddy, B.G.Moates, D.B.Kim, H.-B.Green, T.J.Kim, C.-Y.Terwilliger, T.C.DeLucas, L.J. Tags: Mycobacterium tuberculosis Rv3902c virulence-factor chaperone novel fold structural communications Source Type: research

The structures of the CutA1 proteins from Thermus thermophilus and Pyrococcus horikoshii: characterization of metal-binding sites and metal-induced assembly
CutA1 (copper tolerance A1) is a widespread cytoplasmic protein found in archaea, bacteria, plants and animals, including humans. In Escherichia coli it is implicated in divalent metal tolerance, while the mammalian CutA1 homologue has been proposed to mediate brain enzyme acetylcholinesterase activity and copper homeostasis. The X-ray structures of CutA1 from the thermophilic bacterium Thermus thermophilus (TtCutA1) with and without bound Na+ at 1.7 and 1.9 Å resolution, respectively, and from the hyperthermophilic archaeon Pyrococcus horikoshii (PhCutA1) in complex with Na+ at 1.8 Å resolution have been d...
Source: Acta Crystallographica Section F - March 24, 2014 Category: Biochemistry Authors: Bagautdinov, B. Tags: metal – protein binding copper tolerance β -bulge dodecamer hexa-aquated sodium ion structural communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the Fab portion of the Alzheimer's disease immunotherapy candidate bapineuzumab complexed with amyloid-β
Bapineuzumab (AAB-001) and its derivative (AAB-003) are humanized versions of the anti-Aβ murine antibody 3D6 and are immunotherapy candidates in Alzheimer's disease. The common Fab fragment of these immunotherapies has been expressed, purified and crystallized in complex with β-amyloid peptides (residues 1–8 and 1–28). Diffraction data at high resolution were acquired from crystals of Fab–Aβ8 (2.0 Å) and Fab–Aβ28 (2.2 Å) complexes at the Australian Synchrotron. Both crystal forms belonged to the primitive orthorhombic space group P21221. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 20, 2014 Category: Biochemistry Authors: Crespi, G.A.N.Ascher, D.B.Parker, M.W.Miles, L.A. Tags: bapineuzumab crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of a novel haemagglutinin component of the toxin complex of serotype C Clostridium botulinum
The botulinum toxin complex, the causative agent of botulism, passes through the intestinal wall via sugar-chain-dependent cell binding of a haemagglutinin of 33 kDa molecular weight (HA-33). The amino-acid sequence of the C-terminal half of HA-33 of the serotype C strain Yoichi (C-Yoichi) shares only 46% identity with those of the major serotype C strains. Additionally, C-Yoichi HA-33 exhibits a unique sugar-binding specificity. In the present work, C-Yoichi HA-33 was expressed in Escherichia coli and crystallized. Diffraction data were collected at a resolution of 2.2 Å. The crystals belonged to space group R3....
Source: Acta Crystallographica Section F - February 20, 2014 Category: Biochemistry Authors: Hayashi, S.Akiyama, T.Sagane, Y.Miyashita, S.-I.Watanabe, T.Yajima, S.Niwa, K. Tags: Clostridium botulinum haemagglutinin botulinum toxin complex sugar recognition crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the diterpene cyclooctatin synthase (CYC) from Streptomyces sp. LZ35
Terpenoids are a large and highly diverse group of natural products, with the most chemically diverse pool of structures. Terpene synthase is the key enzyme in the process of terpenoid synthesis. In this paper, the first diterpene synthase (CYC) of bacterial origin was successfully crystallized. Native and SeMet-derivative crystals diffracted to 1.75 and 2.6 Å resolution, respectively. The native crystal belonged to space group P212121, with unit-cell parameters a = 59.10, b = 101.73, c = 108.93 Å, and contained two molecules per asymmetric unit. The SeMet-derivative crystal belonged to space grou...
Source: Acta Crystallographica Section F - February 20, 2014 Category: Biochemistry Authors: Zhang, X.Shang, G.Gu, L.Shen, Y. Tags: diterpene cyclooctatin synthase (CYC) terpene synthases Streptomyces sp. LZ35 crystallization communications Source Type: research

A range of C∊3–C∊4 interdomain angles in IgE Fc accommodate binding to its receptor CD23
The antibody IgE plays a central role in allergic disease, functioning principally through two cell-surface receptors: Fc∊RI and CD23. Fc∊RI on mast cells and basophils mediates the immediate hypersensitivity response, whilst the interaction of IgE with CD23 on B cells regulates IgE production. Crystal structures of the lectin-like `head' domain of CD23 alone and bound to a subfragment of IgE consisting of the dimer of C∊3 and C∊4 domains (Fc∊3-4) have recently been determined, revealing flexibility in the IgE-binding site of CD23. Here, a new crystal form of the CD23–Fc∊3-4 complex with different molecul...
Source: Acta Crystallographica Section F - February 20, 2014 Category: Biochemistry Authors: Dhaliwal, B.Pang, M.O.Y.Yuan, D.Beavil, A.J.Sutton, B.J. Tags: immunoglobin E CD23 Fc ∊ 3-4 structural communications Source Type: research

Nucleation precursors in protein crystallization
Protein crystal nucleation is a central problem in biological crystallography and other areas of science, technology and medicine. Recent studies have demonstrated that protein crystal nuclei form within crucial precursors. Here, methods of detection and characterization of the precursors are reviewed: dynamic light scattering, atomic force microscopy and Brownian microscopy. Data for several proteins provided by these methods have demonstrated that the nucleation precursors are clusters consisting of protein-dense liquid, which are metastable with respect to the host protein solution. The clusters are several hundred nano...
Source: Acta Crystallographica Section F - February 19, 2014 Category: Biochemistry Authors: Vekilov, P.G.Vorontsova, M.A. Tags: nucleation mechanism crystallization protein crystals two-step nucleation protein-rich clusters partial unfolding crystallization communications Source Type: research

Combining secondary-structure and protein solvent-accessibility predictions in methionine substitution for anomalous dispersion
In this study, several leucine and isoleucine residues were selected for methionine substitution by combining secondary-structure and solvent-accessibility predictions. From the secondary-structure prediction, mutated residues were first determined in the coil or loop regions at the junction of two secondary structures. Since leucine and isoleucine residues are hydrophobic and are normally buried within the protein core, these residues should have a higher solvent-accessibility prediction so that they would be partially buried or exposed in the protein. In addition, five residues (Leu107, Leu202, Ile133, Leu128 and Ile159)...
Source: Acta Crystallographica Section F - February 19, 2014 Category: Biochemistry Authors: Wu, H.-Y.Cheng, Y.-S. Tags: Arabidopsis thaliana thylakoid lumen protein anomalous dispersion multi-wavelength anomalous diffraction MAD single-wavelength anomalous diffraction SAD methionine substitution solvent accessibility protein solvent-accessible surface-area Source Type: research

Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis
In Gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a five-protein β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved integral outer membrane protein. Here, the refolding, crystallization and preliminary X-ray crystallographic characterization of the β-barrel domain of BamA from Escherichia coli (EcBamA) are reported. Native and selenomethionine-substituted EcBamA proteins were crystallized at 16°C and X-ray diffraction data were collected to 2.6 and 3.7 Å resolution, respectively. The native crystals belonged to space g...
Source: Acta Crystallographica Section F - February 19, 2014 Category: Biochemistry Authors: Ni, D.Yang, K.Huang, Y. Tags: BamA protein refolding β -barrel outer membrane protein outer membrane protein biogenesis crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the interleukin-3 alpha receptor bound to the Fab fragment of antibody CSL362
Interleukin-3 (IL-3) is a member of the beta common family of cytokines that regulate multiple functions of myeloid cells. The IL-3 receptor-specific alpha subunit (IL3Rα) is overexpressed on stem cells/progenitor cells of patients with acute myeloid leukaemia, where elevated receptor expression correlates clinically with a reduced patient survival rate. The monoclonal antibody (MAb) CSL362 is a humanized MAb derived from the murine MAb 7G3, originally identified for its ability to specifically recognize the human IL-3 receptor and for blocking the signalling of IL-3 in myeloid and endothelial cells. In order to eluc...
Source: Acta Crystallographica Section F - February 19, 2014 Category: Biochemistry Authors: Broughton, S.E.Hercus, T.R.Nero, T.L.Dhagat, U.Owczarek, C.M.Hardy, M.P.Fabri, L.J.Scotney, P.D.Nash, A.D.Wilson, N.J.Lopez, A.F.Parker, M.W. Tags: cytokines interleukin-3 IL-3 receptor-specific alpha subunit crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray diffraction analysis of the kinase domain of human tousled-like kinase 2
Tousled-like kinases (TLKs) are an evolutionarily conserved family of serine/threonine protein kinases involved in chromatin dynamics, including DNA replication and repair, transcription and chromosome segregation. The two members of the family reported in humans, namely TLK1 and TLK2, localize to the cell nucleus and are capable of forming homo- or hetero-oligomers by themselves. To characterize the role of TLK2, its C-terminal kinase domain was cloned and overexpressed in Escherichia coli followed by purification to homogeneity. Crystallization experiments in the presence of ATP-γ-S yielded crystals suitable for X-...
Source: Acta Crystallographica Section F - February 19, 2014 Category: Biochemistry Authors: Garrote, A.M.Redondo, P.Montoya, G.Muñoz, I.G. Tags: human tousled-like kinase 2 crystallization communications Source Type: research

Crystallization and preliminary X-ray analysis of the catalytic domains of Paenibacillus sp. strain FPU-7 cell-surface-expressed chitinase ChiW
The polysaccharide chitin is effectively hydrolyzed and utilized as a carbon and nitrogen source by the Gram-positive bacterium Paenibacillus sp. strain FPU-7. ChiW is a unique cell-surface-expressed chitinase among the Paenibacillus sp. strain FPU-7-secreted chitinases. An N-terminally truncated ChiW protein, primarily comprised of the two catalytic domains of the full-length protein, was successfully overexpressed in Escherichia coli, purified as a functional recombinant protein with a molecular mass of approximately 98 kDa and crystallized. Preliminary X-ray analysis showed that the crystal diffracted to 1.93 Å...
Source: Acta Crystallographica Section F - February 19, 2014 Category: Biochemistry Authors: Itoh, T.Hibi, T.Sugimoto, I.Suzuki, F.Fujii, Y.Taketo, A.Kimoto, H. Tags: ChiW cell-surface-expressed chitinase Paenibacillus sp. strain FPU-7 crystallization communications Source Type: research

Tetartohedral twinning in IDI-2 from Thermus thermophilus: crystallization under anaerobic conditions
In this study, the protein was expressed and purified under aerobic conditions and then reduced and crystallized under anaerobic conditions. Crystals grown by the sitting-drop vapour-diffusion method and then soaked with IPP diffracted to 2.1 Å resolution and belonged to the hexagonal space group P6322, with unit-cell parameters a = b = 133.3, c = 172.9 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - February 19, 2014 Category: Biochemistry Authors: de Ruyck, J.Schubert, H.L.Janczak, M.W.Poulter, C.D. Tags: isopentenyl diphosphate isomerase IDI-2 flavoprotein anaerobic isoprenoid twinning crystallization communications Source Type: research