Purification, crystallization and preliminary X-ray crystallographic analysis of the flagellar accessory protein FlaH from the methanogenic archaeon Methanocaldococcus jannaschii
The flagellar accessory protein FlaH is thought to be one of the essential components of an archaeal motility system. However, to date biochemical and structural information about this protein has been limited. Here, the crystallization of FlaH from the hyperthermophilic archaeon Methanocaldococcus jannaschii is reported. Protein crystals were obtained by the vapour-diffusion method. These crystals belonged to space group P3121, with unit-cell parameters a = b = 131.42, c = 89.35 Å. The initial solution of the FlaH structure has been determined by multiple-wavelength anomalous dispersion phasing using a selenomethi...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Meshcheryakov, V.A.Yoon, Y.-H.Matsunami, H.Wolf, M. Tags: FlaH Methanocaldococcus jannaschii crystallization communications Source Type: research

Purification, crystallization and preliminary crystallographic investigation of FrnE, a disulfide oxidoreductase from Deinococcus radiodurans
In prokaryotes, Dsb proteins catalyze the formation of native disulfide bonds through an oxidative folding pathway and are part of the cell machinery that protects proteins from oxidative stress. Deinococcus radiodurans is an extremophile which shows unparalleled resistance to ionizing radiation and oxidative stress. It has a strong mechanism to protect its proteome from oxidative damage. The genome of Deinococcus shows the presence of FrnE, a Dsb protein homologue that potentially provides the bacterium with oxidative stress tolerance. Here, crystallization and preliminary X-ray crystallographic analysis of FrnE from D. r...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Panicker, L.Misra, H.S.Bihani, S.C. Tags: Deinococcus radiodurans FrnE disulfide oxidoreductase oxidative stress Dsb proteins crystallization communications Source Type: research

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the extracellular olfactomedin domain of gliomedin
Gliomedin (GLDN) is one of the essential proteins in the development of the nodes of Ranvier in the vertebrate peripheral nervous system. An olfactomedin (OLF) domain is located at the GLDN extracellular C-terminus and is involved in the accumulation of neuronal plasma membrane voltage-gated sodium channels in the nodes by interacting with neurofascin and NrCAM. No structures of OLF domains have previously been reported. Here, the crystallization of the rat GLDN OLF domain, which was expressed in an insect-cell system, is reported. The crystal diffracted to 1.55 Å resolution and belonged to space group P21, with un...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Han, H.Kursula, P. Tags: olfactomedin Schwann cell gliomedin myelin cell adhesion crystallization communications Source Type: research

In situ proteolysis, crystallization and preliminary X-ray diffraction analysis of a VHH that binds listeria internalin B
The variable region of camelid heavy-chain antibodies produces the smallest known antibody fragment with antigen-binding capability (a VHH). The VHH R303 binds internalin B (InlB), a virulence factor expressed by the pathogen Listeria monocytogenes. InlB is critical for initiation of Listeria infection, as it binds a receptor (c-Met) on epithelial cells, triggering the entry of bacteria into host cells. InlB is surface-exposed and is required for virulence, hence a VHH targeting InlB has potential applications for pathogen detection or therapeutic intervention. Here, the expression, purification, crystallization and X-ray ...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Huh, I.Gene, R.Kumaran, J.MacKenzie, C.R.Brooks, C.L. Tags: single-domain antibodies VHH nanobodies Listeria monocytogenes virulence factor crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction data of β-galactosidase from Aspergillus niger
β-Galactosidase from Aspergillus niger (An-β-Gal), belonging to the family 35 glycoside hydrolases, hydrolyzes the β-galactosidase linkages in lactose and other galactosides. It is extensively used in industry owing to its high hydrolytic activity and safety. The enzyme has been expressed in yeasts and purified by immobilized metal-ion affinity chromatography for crystallization experiments. The recombinant An-β-Gal, deglycosylated to avoid heterogeneity of the sample, has a molecular mass of 109 kDa. Rod-shaped crystals grew using PEG 3350 as the main precipitant agent. A diffraction data set was col...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Rico-Díaz, A.Vizoso Vázquez, Á.Cerdán, M.E.Becerra, M.Sanz-Aparicio, J. Tags: β -galactosidase glycosidase hydrolase family 35 Aspergillus niger crystallization communications Source Type: research

Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin
Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3121, wi...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Jagadeesan, G.Malathy, P.Gunasekaran, K.Harikrishna Etti, S.Aravindhan, S. Tags: avian haemoglobin great cormorant Phalacrocorax carbo molecular replacement crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic analysis of an artificial molten-globular-like triosephosphate isomerase protein of mixed phylogenetic origin
In this report, the ccTIM protein was successfully crystallized using the microbatch-under-oil method and a full X-ray diffraction data set was collected to 2.2 Å resolution using a synchrotron-radiation source. The crystals belonged to space group C2221, with unit-cell parameters a = 107.97, b = 187.21, c = 288.22 Å. Matthews coefficient calculations indicated the presence of six dimers in the asymmetric unit, with an approximate solvent content of 46.2%. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Goyal, V.D.Yadav, P.Kumar, A.Ghosh, B.Makde, R.D. Tags: protein engineering triosephosphate isomerase consensus design molten globule crystallization communications Source Type: research

Overproduction, crystallization and preliminary X-ray crystallographic analysis of Escherichia coli tRNA N6-threonylcarbamoyladenosine dehydratase
Escherichia coli tRNA N6-threonylcarbamoyladenosine dehydratase (TcdA), previously called CsdL or YgdL, was overproduced and purified from E. coli and crystallized using polyethylene glycol 3350 as a crystallizing agent. X-ray diffraction data were collected to 2.70 Å resolution under cryoconditions using synchrotron X-rays. The crystals belonged to space group P21, with unit-cell parameters a = 65.4, b = 96.8, c = 83.3 Å, β = 111.7°. According to the Matthews coefficient, the asymmetric unit may contain up to four subunits of the monomeric protein, with a crystal volume per protein mass (VM) of 2....
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Kim, S.Kim, K.Y.Park, J.K.Lee, B.I.Kim, Y.-G.Park, S. Tags: tRNA hypermodification N6-threonylcarbamoyladenosine dehydratase TcdA CsdL crystallization communications Source Type: research

Cloning, expression, purification, crystallization and preliminary X-ray characterization of allantoinase from Bacillus licheniformis ATCC 14580
Allantoinase, a member of the amidohydrolase superfamily, exists in a wide variety of organisms, including bacteria, fungi, plants and a few animals, such as fishes and amphibians. Allantoinase catalyzes the reversible hydrolysis of allantoin into allantoate by hydrolytic cleavage of the N1—C2 amide bond of the five-membered hydantoin ring. Allantoinase from Bacillus licheniformis (AllBali) presents an inverted enantioselectivity towards allantoin (R-enantioselective), which is a distinguishable feature that is not observed for other allantoinases. In this work, B. licheniformis ATCC 14580 allantoinase (AllBali) cont...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Conejero-Muriel, M.Martínez-Gómez, A.I.Martínez-Rodríguez, S.Gavira, J.A. Tags: amidohydrolase allantoinase Bacillus licheniformis crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray diffraction analysis of NADP-dependent glutamate dehydrogenase from Aspergillus niger
In this study, Aspergillus niger NADP-GDH (AnGDH) has been overexpressed and purified. Purified AnGDH, with a high specific activity of 631.1 units per milligram of protein, was crystallized and the crystal diffracted to 2.9 Å resolution using a home X-ray source. Preliminary analysis of the X-ray diffraction data showed that the crystal belonged to space group R32, with unit-cell parameters a = b = 173.8, c = 241.5 Å, α = β = 90, γ = 120°. The crystals exhibited an unusually high solvent content (83.0%) and had only one molecule in the asymmetric unit. Initial phases were obtained by m...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Prakash, P.Walvekar, A.S.Punekar, N.S.Bhaumik, P. Tags: glutamate dehydrogenase Aspergillus niger crystallization communications Source Type: research

Production, crystallization and preliminary X-ray diffraction of the Gαs α-helical domain in complex with a nanobody
GPCR–G-protein complexes are one of the most important components of cell-signalling cascades. Extracellular signals are sensed by membrane-associated G-protein-coupled receptors (GPCRs) and transduced via G proteins towards intracellular effector molecules. Structural studies of these transient complexes are crucial to understand the molecular details of these interactions. Although a nucleotide-free GPCR–G-protein complex is stable, it is not an ideal sample for crystallization owing to the intrinsic mobility of the Gαs α-helical domain (AHD). To stabilize GPCR–G-protein complexes in a nucle...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Triest, S.Wohlkönig, A.Pardon, E.Steyaert, J. Tags: GPCR transmembrane signalling nanobody-enabled X-ray crystallography G protein crystallization communications Source Type: research

Structure of type II dehydroquinase from Pseudomonas aeruginosa
Pseudomonas aeruginosa causes opportunistic infections and is resistant to most antibiotics. Ongoing efforts to generate much-needed new antibiotics include targeting enzymes that are vital for P. aeruginosa but are absent in mammals. One such enzyme, type II dehydroquinase (DHQase), catalyzes the interconversion of 3-dehydroquinate and 3-dehydroshikimate, a necessary step in the shikimate pathway. This step is vital for the proper synthesis of phenylalanine, tryptophan, tyrosine and other aromatic metabolites. The recombinant expression, purification and crystal structure of catalytically active DHQase from P. aeruginosa ...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Reiling, S.Kelleher, A.Matsumoto, M.M.Robinson, G.Asojo, O.A. Tags: type II dehydroquinase Pseudomonas aeruginosa shikimate pathway structural communications Source Type: research

The structure of rice weevil pectin methylesterase
Rice weevils (Sitophilus oryzae) use a pectin methylesterase (EC 3.1.1.11), along with other enzymes, to digest cell walls in cereal grains. The enzyme is a right-handed β-helix protein, but is circularly permuted relative to plant and bacterial pectin methylesterases, as shown by the crystal structure determination reported here. This is the first structure of an animal pectin methylesterase. Diffraction data were collected to 1.8 Å resolution some time ago for this crystal form, but structure solution required the use of molecular-replacement techniques that have been developed and similar structures that ha...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Teller, D.C.Behnke, C.A.Pappan, K.Shen, Z.Reese, J.C.Reeck, G.R.Stenkamp, R.E. Tags: Sitophilus oryzae rice weevil pectin methylesterase structural communications Source Type: research

Structure of the methanofuran/methanopterin-biosynthetic enzyme MJ1099 from Methanocaldococcus jannaschii
Prior studies have indicated that MJ1099 from Methanocaldococcus jannaschii has roles in the biosynthesis of tetrahydromethanopterin and methanofuran, two key cofactors of one-carbon (C1) metabolism in diverse organisms including the methanogenic archaea. Here, the structure of MJ1099 has been solved to 1.7 Å resolution using anomalous scattering methods. The results indicate that MJ1099 is a member of the TIM-barrel superfamily and that it is a homohexamer. Bioinformatic analyses identified a potential active site that is highly conserved among MJ1099 homologs and the key amino acids involved were identified. The ...
Source: Acta Crystallographica Section F - October 25, 2014 Category: Biochemistry Authors: Bobik, T.A.Morales, E.J.Shin, A.Cascio, D.Sawaya, M.R.Arbing, M.Yeates, T.O.Rasche, M.E. Tags: methanofuran methanopterin Methanocaldococcus jannaschii MJ1099 structural communications Source Type: research

New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations
Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase from Streptococcus pneumoniae D39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groups P21 and P1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space group C2, with unit-cell parameters a = 73.5, b = 54.3, c = 62.7 &A...
Source: Acta Crystallographica Section F - October 24, 2014 Category: Biochemistry Authors: Thach, T.T.Lee, S. Tags: adenylate kinase Streptococcus pneumoniae ligand-free inhibitor-bound structural communications Source Type: research

Felix Frolow (1947–2014)
(Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 30, 2014 Category: Biochemistry Authors: Livnah, O.Shimon, L. Tags: obituary Felix Frolow obituaries Source Type: research

A drunken search in crystallization space
The REMARK280 field of the Protein Data Bank is the richest open source of successful crystallization information. The REMARK280 field is optional and currently uncurated, so significant effort needs to be applied to extract reliable data. There are well over 15 000 crystallization conditions available commercially from 12 different vendors. After putting the PDB crystallization information and the commercial cocktail data into a consistent format, these data are used to extract information about the overlap between the two sets of crystallization conditions. An estimation is made as to which commercially available condi...
Source: Acta Crystallographica Section F - September 30, 2014 Category: Biochemistry Authors: Fazio, V.J.Peat, T.S.Newman, J. Tags: crystallization crystallization space crystallization communications Source Type: research

Enhancing ubiquitin crystallization through surface-entropy reduction
Ubiquitin has many attributes suitable for a crystallization chaperone, including high stability and ease of expression. However, ubiquitin contains a high surface density of lysine residues and the doctrine of surface-entropy reduction suggests that these lysines will resist participating in packing interactions and thereby impede crystallization. To assess the contributions of these residues to crystallization behavior, each of the seven lysines of ubiquitin was mutated to serine and the corresponding single-site mutant proteins were expressed and purified. The behavior of these seven mutants was then compared with that ...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Loll, P.J.Xu, P.Schmidt, J.T.Melideo, S.L. Tags: ubiquitin surface-entropy reduction laboratory communications Source Type: research

Crystallization and preliminary X-ray diffraction studies of the C-terminal domain of Chlamydia trachomatis CdsD
The inner membrane ring of the bacterial type III secretion system (TTSS) is composed of two proteins. In Chlamydia trachomatis this ring is formed by CdsD (gene name CT_664) and CdsJ (gene name CTA_0609). CdsD consists of 829 amino acids. The last 400 amino acids at its C-terminal end relate it to the type III secretion system YscD/HrpQ protein family. The C-terminal domain, consisting of amino acids 558–771, of C. trachomatis CdsD was overexpressed in Escherichia coli and purified using immobilized metal-affinity chromatography (IMAC) and size-exclusion chromatography. The protein was crystallized using the vapour-...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Meriläinen, G.Wierenga, R.K. Tags: type III secretion system Chlamydia CdsD crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of full-length spr1814, a response regulator of Streptococcus pneumoniae, in complex with a phosphoryl analogue
Spr1814 of Streptococcus pneumoniae is a signal transduction response regulator belonging to the NarL/FixJ subfamily, which has a helix–turn–helix DNA-binding effector domain. To understand how the phosphorylation of the conserved aspartic acid residue induces conformational changes in spr1814 allowing binding to the target promoter, recombinant spr1814 expressed in Escherichia coli was crystallized with the phosphoryl analogue beryllium fluoride BeF3− by the hanging-drop vapour-diffusion method. The crystals diffracted to 1.9 Å resolution and belonged to space group P21, with unit-cell parameters...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Park, A.Oh, J.S.Chi, Y.M.Jeong, S.W. Tags: Streptococcus pneumoniae Spr1814 crystallization communications Source Type: research

Production, crystallization and preliminary crystallographic analysis of Allochromatium vinosum thiosulfate dehydrogenase TsdA, an unusual acidophilic c-type cytochrome
The ability to perform the very simple oxidation of two molecules of thiosulfate to tetrathionate is widespread among prokaryotes. Despite the prevalent occurrence of tetrathionate formation and its well documented significance within the sulfur cycle, little is known about the enzymes that catalyze the oxidative condensation of two thiosulfate anions. To fill this gap, the thiosulfate dehydrogenase (TsdA) enzyme from the purple sulfur bacterium Allochromatium vinosum was recombinantly expressed in Escherichia coli, purified and crystallized, and a crystallographic data set was collected. The crystals belonged to the monoc...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Brito, J.A.Gutierres, A.Denkmann, K.Dahl, C.Archer, M. Tags: thiosulfate dehydrogenase Allochromatium vinosum c-type cytochrome sulfur metabolism crystallization communications Source Type: research

Crystallization and preliminary crystallographic analysis of poly(3-hydroxybutyrate) depolymerase from Bacillus thuringiensis
Poly[(R)-3-hydroxybutyrate] (PHB) is a microbial biopolymer that has been commercialized as biodegradable plastics. The key enzyme for the degradation is PHB depolymerase (PhaZ). A new intracellular PhaZ from Bacillus thuringiensis (BtPhaZ) has been screened for potential applications in polymer biodegradation. Recombinant BtPhaZ was crystallized using 25% polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M bis-tris pH 6.5 at 288 K. The crystals belonged to space group P1, with unit-cell parameters a = 42.97, b = 83.23, c = 85.50 Å, α = 73.45, β = 82.83, γ = 83.49°. An X-ray diffracti...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Wang, Y.-L.Lin, Y.-T.Chen, C.-L.Shaw, G.-C.Liaw, S.-H. Tags: poly(3-hydroxybutyrate) depolymerase PhaZ Bacillus thuringiensis crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of a novel sphingomyelinase D from Loxosceles gaucho venom
Brown spider envenomation results in dermonecrosis, intravascular coagulation, haemolysis and renal failure, mainly owing to the action of sphingomyelinases D (SMases D), which catalyze the hydrolysis of sphingomyelin to produce ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidylcholine to produce lysophosphatidic acid. Here, the heterologous expression, purification, crystallization and preliminary X-ray diffraction analysis of LgRec1, a novel SMase D from Loxosceles gaucho venom, are reported. The crystals belonged to space group P21212, with unit-cell parameters a = 52.98, b = 62.27, c = 84.84 &Arin...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Ullah, A.Magalhães, G.S.Masood, R.Mariutti, R.B.Coronado, M.A.Murakami, M.T.Barbaro, K.C.Arni, R.K. Tags: sphingomyelinase D Loxosceles gaucho crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic studies of Drep2 CIDE domain
In this study, the Drep2 CIDE domain was purified and crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were then collected to a resolution of 2.3 Å. The crystals were found to belong to the orthorhombic space group P212121, with unit-cell parameters a = 50.28, b = 88.70, c = 113.37 Å. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Lee, S.M.Park, H.H. Tags: apoptosis DNA fragmentation factor CIDE domain Drep2 Drosophila melanogaster crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of cyclolavandulyl diphosphate synthase, a new member of the cis-isoprenyl diphosphate synthase superfamily
Cyclolavandulyl diphosphate synthase (CLDS; estimated molecular weight 23.1 kDa) from the soil bacterium Streptomyces sp. CL190 is an enzyme that catalyzes both the condensation of two molecules of C5 dimethylallyl diphosphate (DMAPP) and the subsequent cyclization. CLDS was crystallized in the absence and the presence of the substrate DMAPP. Diffraction data were collected at a synchrotron source and the crystals diffracted to 2.00 and 1.73 Å resolution, respectively. The crystal obtained in the absence of DMAPP belonged to space group P212121, with unit-cell parameters a = 39.0, b = 87.5, c = 113.6 Å. T...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Tomita, T.Ozaki, T.Matsuda, K.Nishiyama, M.Kuzuyama, T. Tags: condensing enzyme cyclase cyclolavandulyl diphosphate synthase Streptomyces sp. CL190 terpene crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analyses of the redox-controlled complex of terminal oxygenase and ferredoxin components in the Rieske nonhaem iron oxygenase carbazole 1,9a-dioxygenase
The initial reaction in bacterial carbazole degradation is catalyzed by carbazole 1,9a-dioxygenase, which consists of terminal oxygenase (Oxy), ferredoxin (Fd) and ferredoxin reductase components. The electron-transfer complex between reduced Oxy and oxidized Fd was crystallized at 293 K using the hanging-drop vapour-diffusion method with PEG 3350 as the precipitant under anaerobic conditions. The crystal diffracted to a maximum resolution of 2.25 Å and belonged to space group P21, with unit-cell parameters a = 97.3, b = 81.6, c = 116.2 Å, α = γ = 90, β = 100.1°. The VM value is 2.85...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Matsuzawa, J.Aikawa, H.Umeda, T.Ashikawa, Y.Suzuki-Minakuchi, C.Kawano, Y.Fujimoto, Z.Okada, K.Yamane, H.Nojiri, H. Tags: Rieske nonhaem iron oxygenase electron-transfer complex terminal oxygenase ferredoxin carbazole 1,9a-dioxygenase crystallization communications Source Type: research

Expression, crystallization and preliminary X-ray analysis of McbB, a multifunctional enzyme involved in β-carboline skeleton biosynthesis
β-Carboline alkaloids (βCs), with tricyclic pyrido[3,4-b]indole rings, have important pharmacological and therapeutic value. In the biosynthesis of βCs, the Pictet–Spengler (PS) cyclization reaction is responsible for the formation of ring structures. McbB is one of a few enzymes that are known to catalyse PS cyclization. It can also catalyse decarboxylation and oxidation. Here, the expression, crystallization and preliminary data analysis of McbB are reported. The crystals diffracted to 2.10 Å resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 66.06, b = 8...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Wang, H.Zhang, H.Mi, Y.Ju, J.Chen, Q.Zhang, H. Tags: β -carboline alkaloids Pictet – Spengler cyclization McbB Marinactinospora thermotolerans crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of Lin1840, a putative β-glucosidase from Listeria innocua
Lin1840 is a putative β-glucosidase that is predicted to be involved in 1,2-β-glucan metabolism since the lin1839 gene encoding a 1,2-β-oligoglucan phosphorylase and the lin1840 gene are located in the same gene cluster. Here, Lin1840 was crystallized. The crystals of Lin1840 diffracted to beyond 1.8 Å resolution. The crystal belonged to space group I121, with unit-cell parameters a = 89.75, b = 95.10, c = 215.00 Å, α = 90.00, β = 96.34, γ = 90.00°. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Nakajima, M.Yoshida, R.Miyanaga, A.Taguchi, H. Tags: β -glucosidase 1,2- -glucan crystallization communications Source Type: research

Cloning, expression, purification and preliminary X-ray analysis of EstN2, a novel archaeal α/β-hydrolase from Candidatus Nitrososphaera gargensis
EstN2 is a novel α/β-hydrolase originating from the ammonia-oxidizing thaumarchaeon Candidatus Nitrososphaera gargensis. The genome of the organism was sequenced and genes conferring putative lipolytic activity were amplified and cloned into Escherichia coli as a heterologous host. Through function-based screening, esterase and lipase activity was detected. A recombinant enzyme designated EstN2 was successfully expressed, purified and crystallized. The crystals belonged to space group I2, with one molecule per asymmetric unit, and diffracted X-rays to 1.5 Å resolution. (Source: Acta Crystallographica Section F)
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Kaljunen, H.Chow, J.Streit, W.R.Mueller-Dieckmann, J. Tags: EstN2 α / β -hydrolase Candidatus Nitrososphaera gargensis crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the BRPF1 bromodomain in complex with its H2AK5ac and H4K12ac histone-peptide ligands
The bromodomain-PHD finger protein 1 (BRPF1) is an essential subunit of the monocytic leukemia zinc (MOZ) histone acetyltransferase (HAT) complex and is required for complex formation and enzymatic activation. BRPF1 contains a structurally conserved bromodomain, which recognizes specific acetyllysine residues on histone proteins. The MOZ HAT plays a direct role in hematopoiesis, and deregulation of its activity is linked to the development of acute myeloid leukemia. However, the molecular mechanism of histone-ligand recognition by the BRPF1 bromodomain is currently unknown. The 117-amino-acid BRPF1 bromodomain was overexpr...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Lubula, M.Y.Poplawaski, A.Glass, K.C. Tags: BRPF1 bromodomain H4K12ac H2AK5ac crystallization communications Source Type: research

Crystallization and preliminary X-ray crystallographic studies of CrArsM, an arsenic(III) S-adenosylmethionine methyltransferase from Chlamydomonas reinhardtii
Arsenic is one the most toxic environmental substances. Arsenic is ubiquitous in water, soil and food, and ranks first on the Environmental Protection Agency's Superfund Priority List of Hazardous Substances. Arsenic(III) S-adenosylmethionine methyltransferases (AS3MT in animals and ArsM in microbes) are key enzymes of arsenic biotransformation, catalyzing the methylation of inorganic arsenite to give methyl, dimethyl and trimethyl products. Arsenic methyltransferases are found in members of every kingdom from bacteria to humans (EC 2.1.1.137). In the human liver, hAS3MT converts inorganic arsenic into more toxic and carci...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Packianathan, C.Pillai, J.K.Riaz, A.Kandavelu, P.Sankaran, B.Rosen, B.P. Tags: S-adenosylmethionine methyltransferase Chlamydomonas reinhardtii crystallization communications Source Type: research

Crystallization of the Ets1–Runx1–CBFβ–DNA complex formed on the TCRα gene enhancer
Gene transcription is regulated in part through the assembly of multiple transcription factors (TFs) on gene enhancers. To enable examination of the mechanism underlying the formation of these complexes and their response to a phosphorylation signal, two kinds of higher-order TF–DNA assemblies were crystallized composed of an unmodified or phosphorylated Ets1 fragment, a Runx1(L94K) fragment and a CBFβ fragment on the T-cell receptor (TCR) α gene enhancer. Within these complexes, the Ets1 and Runx1 fragments contain intrinsically disordered regulatory regions as well as their DNA-binding domains. Crystals ...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Shiina, M.Hamada, K.Inoue-Bungo, T.Shimamura, M.Baba, S.Sato, K.Ogata, K. Tags: Runx1 Ets1 CBF β TCR gene enhancer chemical modification transcription crystallization communications Source Type: research

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of fructose-1,6-bisphosphate aldolase from Escherichia coli
Fructose-1,6-bisphosphate aldolase is one of the most important enzymes in the glycolytic pathway and catalyzes the reversible cleavage of fructose-1,6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. The full-length fbaB gene encoding fructose-1,6-bisphosphate aldolase class I (FBPA I) was cloned from Escherichia coli strain BL21. FBPA I was overexpressed in E. coli and purified. Biochemical analysis found that the optimum reaction temperature of FBPA I is 330.5 K and that the enzyme has a high temperature tolerance. Crystals of recombinant FBPA I were obtained by the sitting-drop vapour-diffus...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Zhang, L.Guo, Z.Huang, J.Liu, M.Wang, Y.Ji, C. Tags: thermostability Ec-FBPA I fructose-1,6-bisphosphate aldolase crystallization communications Source Type: research

Purification and X-ray crystallographic analysis of 7-keto-8-aminopelargonic acid (KAPA) synthase from Mycobacterium smegmatis
7-Keto-8-aminopelargonic acid synthase (KAPA synthase; BioF) is an essential enzyme for mycobacterial growth that catalyses the first committed step in the biotin-synthesis pathway. It is a pyridoxal 5′-phosphate (PLP)-dependent enzyme and is a potential drug target. Here, the cloning, expression, purification and crystallization of KAPA synthase from Mycobacterium smegmatis (MsBioF) and the characterization of MsBioF crystals using X-ray diffraction are described. The crystals diffracted to 2.3 Å resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 70.88, b = 91.68, c = 10...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Fan, S.Li, D.Fleming, J.Hong, Y.Chen, T.Zhou, L.Bi, L.Wang, D.Zhang, X.Chen, G. Tags: Mycobacterium smegmatis biotin-synthesis pathway 7-keto-8-aminopelargonic acid (KAPA) synthase crystallization communications Source Type: research

Expression, crystallization and preliminary X-ray crystallographic analysis of cystathionine β-lyase from Acinetobacter baumannii OXA-23
Multidrug-resistant Acinetobacter baumannii (Ab) has emerged as a leading nosocomial pathogen because of its resistance to most currently available antibiotics. Cystathionine β-lyase (CBL), a pyridoxal 5′-phosphate (PLP)-dependent enzyme, catalyzes the second step in the transsulfuration pathway, which is essential for the metabolic interconversion of the sulfur-containing amino acids homocysteine and methionine. The enzymes of the transsulfuration pathway are considered to be attractive drug targets owing to their specificity to microbes and plants. As a potential target for the development of novel antibacteri...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Nguyen, D.-Q.Ngo, H.-P.-T.Ahn, Y.-J.Lee, S.H.Kang, L.-W. Tags: cystathionine β -lyase PLP-dependent enzyme multidrug-resistant Acinetobacter baumannii crystallization communications Source Type: research

Cloning, expression, purification, crystallization and preliminary X-ray diffraction of a lysine-specific permease from Pseudomonas aeruginosa
The prokaryotic lysine-specific permease (LysP) belongs to the amino acid–polyamine–organocation (APC) transporter superfamily. In the cell, members of this family are responsible for the uptake and recycling of nutrients, for the maintenance of a constant internal ion concentration and for cell volume regulation. The detailed mechanism of substrate selectivity and transport of l-lysine by LysP is not understood. A high-resolution crystal structure would enormously facilitate such an understanding. To this end, LysP from Pseudomonas aeruginosa was recombinantly expressed in Escherichia coli and purified to near...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Nji, E.Li, D.Doyle, D.A.Caffrey, M. Tags: APC transporter superfamily GFP fusion LysP membrane protein crystallization communications Source Type: research

Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element
Pax genes belong to a family of metazoan transcription factors that are known to play a critical role in eye, ear, kidney and neural development. The mammalian Pax family of transcription factors is characterized by a ∼128-amino-acid DNA-binding paired domain that makes sequence-specific contacts with DNA. The diversity in Pax gene activities emerges from complex modes of interaction with enhancer regions and heterodimerization with multiple interaction partners. Based on in vitro optimal binding-site selection studies and enhancer identification assays, it has been suggested that Pax proteins may recognize and bind th...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Narasimhan, K.Hilbig, A.Udayasuryan, B.Jayabal, S.Kolatkar, P.R.Jauch, R. Tags: δ -crystallin DC5 enhancer Pax9 paired domain crystallization communications Source Type: research

Purification, crystallization and preliminary X-ray crystallographic analysis of human IL-18 and its extracellular complexes
Interleukin-18 (IL-18), a pro-inflammatory cytokine belonging to the interleukin-1 (IL-1) family, is involved in the pathogenesis of autoimmune/autoinflammatory and allergic diseases such as juvenile idiopathic arthritis and bronchial asthma. IL-18 forms a signalling complex with the IL-18 receptor α (IL-18Rα) and β (IL-18Rβ) chains; however, the detailed activation mechanism remains unclear. Here, the IL-18–IL-18Rα binary and IL-18–IL-18Rα–IL-18Rβ ternary complexes were purified and crystallized as well as IL-18 alone. An X-ray diffraction data set for IL-18 was col...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Kimura, T.Tsutsumi, N.Arita, K.Ariyoshi, M.Ohnishi, H.Kondo, N.Shirakawa, M.Kato, Z.Tochio, H. Tags: interleukin-18 IL-1 superfamily interleukin-18 receptor α β immunity inflammation autoimmunity allergy crystallization communications Source Type: research

Expression, purification and preliminary crystallographic analysis of the cryptic polo-box domain of Caenorhabditis elegans ZYG-1
ZYG-1 is a polo-like kinase essential for centriole assembly in Caenorhabditis elegans. The targeting of ZYG-1 to nascent centrioles is via its central cryptic polo-box (CPB) domain. To shed light on the molecular basis of ZYG-1 recruitment, it is necessary to obtain structural knowledge of the ZYG-1 CPB. Here, the expression, purification and preliminary crystallographic analysis of the ZYG-1 CPB are reported. The protein was overexpressed in Escherichia coli strain BL21 (DE3), purified by multi-step chromatography and crystallized using the vapour-diffusion method. Crystals of the wild-type protein exhibited an order&nda...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Shimanovskaya, E.Dong, G. Tags: centriole cryptic polo-box domain Plk4 polo-like kinase ZYG-1 crystallization communications Source Type: research

Structure of homoserine O-acetyltransferase from Staphylococcus aureus: the first Gram-positive ortholog structure
Homoserine O-acetyltransferase (HTA) catalyzes the formation of l-O-acetyl-homoserine from l-homoserine through the transfer of an acetyl group from acetyl-CoA. This is the first committed step required for the biosynthesis of methionine in many fungi, Gram-positive bacteria and some Gram-negative bacteria. The structure of HTA from Staphylococcus aureus (SaHTA) has been determined to a resolution of 2.45 Å. The structure belongs to the α/β-hydrolase superfamily, consisting of two distinct domains: a core α/β-domain containing the catalytic site and a lid domain assembled into a helical bundle...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Thangavelu, B.Pavlovsky, A.G.Viola, R. Tags: homoserine O-acetyltransferase Staphylococcus aureus α / β -hydrolase methionine biosynthesis structural communications Source Type: research

Structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a conserved cytosolic enzyme, which plays a key role in glycolysis. GAPDH catalyzes the oxidative phosphorylation of d-glyceraldehyde 3-phosphate using NAD or NADP as a cofactor. In addition, GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate. Here, the crystal structure of GBS GAPDH from Streptococcus agalactiae in complex with NAD is reported at 2.46 Å resolution. A...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Ayres, C.A.Schormann, N.Senkovich, O.Fry, A.Banerjee, S.Ulett, G.C.Chattopadhyay, D. Tags: glyceraldehyde 3-phosphate dehydrogenase Streptococcus agalactiae structural communications Source Type: research

Structure of an Aspergillus fumigatus old yellow enzyme (EasA) involved in ergot alkaloid biosynthesis
The Aspergillus fumigatus old yellow enzyme (OYE) EasA reduces chanoclavine-I aldehyde to dihydrochanoclavine aldehyde and works in conjunction with festuclavine synthase at the branchpoint for ergot alkaloid pathways. The crystal structure of the FMN-loaded EasA was determined to 1.8 Å resolution. The active-site amino acids of OYE are conserved, supporting a similar mechanism for reduction of the α/β-unsaturated aldehyde. The C-terminal tail of one monomer packs into the active site of a monomer in the next asymmetric unit, which is most likely to be a crystallization artifact and not a mechanism of se...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Chilton, A.S.Ellis, A.L.Lamb, A.L. Tags: ergot alkaloid old yellow enzyme EasA FgaOx3 Aspergillus fumigatus structural communications Source Type: research

Human carbonic anhydrase II–cyanate inhibitor complex: putting the debate to rest
The binding of anions to carbonic anhydrase II (CA II) has been attributed to high affinity for the active-site zinc. An anion of interest is cyanate, for which contrasting binding modes have been reported in the literature. Previous spectroscopic data have shown cyanate behaving as an inhibitor, directly binding to the zinc, in contrast to previous crystallographic data that implied that cyanate acts as a substrate mimic that is not directly bound to the zinc but overlaps with the binding site of the substrate CO2. Wild-type and the V207I variant of CA II have been expressed and X-ray crystal structures of their cyanate c...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: West, D.Pinard, M.A.Tu, C.Silverman, D.N.McKenna, R. Tags: carbonic anhydrase α -class CA cyanate structural communications Source Type: research

Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii
Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occ...
Source: Acta Crystallographica Section F - September 25, 2014 Category: Biochemistry Authors: Shah, B.S.Tetu, S.G.Harrop, S.J.Paulsen, I.T.Mabbutt, B.C. Tags: opportunistic pathogen Acinetobacter baumannii WM99c nosocomial strain multidrug resistance Rossmann fold structural communications Source Type: research

The structure of lactoferrin-binding protein B from Neisseria meningitidis suggests roles in iron acquisition and neutralization of host defences
Pathogens have evolved a range of mechanisms to acquire iron from the host during infection. Several Gram-negative pathogens including members of the genera Neisseria and Moraxella have evolved two-component systems that can extract iron from the host glycoproteins lactoferrin and transferrin. The homologous iron-transport systems consist of a membrane-bound transporter and an accessory lipoprotein. While the mechanism behind iron acquisition from transferrin is well understood, relatively little is known regarding how iron is extracted from lactoferrin. Here, the crystal structure of the N-terminal domain (N-lobe) of the ...
Source: Acta Crystallographica Section F - September 24, 2014 Category: Biochemistry Authors: Brooks, C.L.Arutyunova, E.Lemieux, M.J. Tags: lactoferrin lactoferricin transferrin LbpB LbpA TbpA TbpB Neisseria meningitidis structural communications Source Type: research

The structure of alanine racemase from Acinetobacter baumannii
Acinetobacter baumannii is an opportunistic Gram-negative bacterium which is a common cause of hospital-acquired infections. Numerous antibiotic-resistant strains exist, emphasizing the need for the development of new antimicrobials. Alanine racemase (Alr) is a pyridoxal 5′-phosphate dependent enzyme that is responsible for racemization between enantiomers of alanine. As d-alanine is an essential component of the bacterial cell wall, its inhibition is lethal to prokaryotes, making it an excellent antibiotic drug target. The crystal structure of A. baumannii alanine racemase (AlrAba) from the highly antibiotic-resista...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Davis, E.Scaletti-Hutchinson, E.Opel-Reading, H.Nakatani, Y.Krause, K. Tags: Acinetobacter baumannii alanine racemase structural communications Source Type: research

Structural analysis of the GH43 enzyme Xsa43E from Butyrivibrio proteoclasticus
The rumen of dairy cattle can be thought of as a large, stable fermentation vat and as such it houses a large and diverse community of microorganisms. The bacterium Butyrivibrio proteoclasticus is a representative of a significant component of this microbial community. It is a xylan-degrading organism whose genome encodes a large number of open reading frames annotated as fibre-degrading enzymes. This suite of enzymes is essential for the organism to utilize the plant material within the rumen as a fuel source, facilitating its survival in this competitive environment. Xsa43E, a GH43 enzyme from B. proteoclasticus, has bee...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Till, M.Goldstone, D.Card, G.Attwood, G.T.Moon, C.D.Arcus, V.L. Tags: Xsa43E GH43 Butyrivibrio proteoclasticus structural communications Source Type: research

Structure of Toxoplasma gondii fructose-1,6-bisphosphate aldolase
The apicomplexan parasite Toxoplasma gondii must invade host cells to continue its lifecycle. It invades different cell types using an actomyosin motor that is connected to extracellular adhesins via the bridging protein fructose-1,6-bisphosphate aldolase. During invasion, aldolase serves in the role of a structural bridging protein, as opposed to its normal enzymatic role in the glycolysis pathway. Crystal structures of the homologous Plasmodium falciparum fructose-1,6-bisphosphate aldolase have been described previously. Here, T. gondii fructose-1,6-bisphosphate aldolase has been crystallized in space group P22121, with ...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Boucher, L.E.Bosch, J. Tags: Toxoplasma aldolase glideosome invasion MIC2 F16BP structural communications Source Type: research

X-ray structures of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana
The chloroplastic Arabidopsis thaliana Nfs2 (AtNfs2) is a group II pyridoxal 5′-phosphate-dependent cysteine desulfurase that is involved in the initial steps of iron–sulfur cluster biogenesis. The group II cysteine desulfurases require the presence of sulfurtransferases such as SufE proteins for optimal activity. Compared with group I cysteine desulfurases, proteins of this group contains a smaller extended lobe harbouring the catalytic cysteine and have a β-hairpin constraining the active site. Here, two crystal structures of AtNfs2 are reported: a wild-type form with the catalytic cysteine in a persulfi...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Roret, T.Pégeot, H.Couturier, J.Mulliert, G.Rouhier, N.Didierjean, C. Tags: cysteine desulfurase iron – sulfur cluster Arabidopsis thaliana SUF machinery structural communications Source Type: research

Structure of Mycobacterium smegmatis Eis in complex with paromomycin
The Rv2416c gene of Mycobacterium tuberculosis (Mtb) encodes the enhanced intracellular survival (Eis) protein that enhances intracellular survival of the pathogen in host macrophages during infection. The Mtb Eis protein is released into the cytoplasm of the phagocyte during intracellular infection and modulates the host immune response. It also contributes to drug resistance by acetylating multiple amine groups of aminoglycosides. Interestingly, the nonpathogenic M. smegmatis (Msm) contains a homologous eis gene (MSMEG_3513). The overall structures of Mtb Eis and Msm Eis are highly similar to each other, reflecting the h...
Source: Acta Crystallographica Section F - August 29, 2014 Category: Biochemistry Authors: Kim, K.H.An, D.R.Yoon, H.J.Yang, J.K.Suh, S.W. Tags: tuberculosis aminoglycoside paromomycin tobramycin drug resistance Mycobacterium smegmatis Mycobacterium tuberculosis structural communications Source Type: research