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September 2012 issue
Cover illustration: Macrophage migration inhibitory factor covalently complexed with phenethylisothiocyanate (Tyndall et al., p. 999).
structural communications
Macrophage migration inhibitory factor undergoes a localized conformational shift in response to covalent modification by phenethyl isothiocyanate, a natural compound with anti-inflammatory and anticancer properties. The inhibitor sits within a deep hydrophobic pocket and defines a potential target for the development of improved inhibitors.
Structure of a UDP-glucose dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum
The crystal structure of an extremely thermostable UDP-glucose dehydrogenase from a hyperthermophile was determined.
PDB reference: UDP-glucose dehydrogenase, 3vtf
The structure of barley limit dextrinase including all flexible loops has been traced at 1.9 Å resolution.
PDB reference: barley limit dextrinase, 4aio
Active-site Phe87 of cytochrome P450 BM3 protects the haem from DMSO molecule, thereby conferring higher organic co-solvent tolerance.
The crystal structure of C. jejuni anabolic ornithine transcarbamoylase has been determined at a resolution of 2.7 Å in an unliganded state.
PDB reference: anabolic ornithine carbamoyltransferase, 3tpf
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The cell-cycle regulator ChpT of C. crescentus is a dimeric histidine phosphotransferase that resembles the typical structure of histidine kinases.
PDB reference: ChpT, 4fpp
crystallization communications
A complex of a mutated ScaB dockerin with the third ScaC cohesin from A. cellulolyticus has been crystallized and data were collected from two different crystal forms to 1.5 and 6.0 Å resolution.
The ligand-binding domain of the transcription factor PqsR from P. aeruginosa has been crystallized and initial phases have been obtained using SAD data from seleno-L-methionine-labelled crystals.
Dihydrodipicolinate synthase from the plant pathogen A. tumefaciens has been cloned, expressed, purified and crystallized in its unliganded form, in the presence of its substrate pyruvate and in the presence of pyruvate and the allosteric inhibitor lysine. Diffraction data for the crystals were collected to a maximum resolution of 1.40 Å.
The cloning, expression and crystallization of a thermophilic ferredoxin–NAD(P)+ reductase were successfully carried out and resulting crystals were suitable for structural determination.
Crotamine from C. durissus terrificus was crystallized and diffraction data were collected to a resolution of 1.9 Å.
The S. cerevisiae V-ATPase subunit F (F1–94) protein and the selenomethionyl form of its I69M mutant protein were produced, purified and crystallized. X-ray diffraction data were collected to resolutions of 2.64 and 2.3 Å, respectively, and the crystals belonged to the orthorhombic space group C2221.
The mature protein of the potent anti-HIV lectin actinohivin has been crystallized with high reproducibility in a new form without packing disorder.
Single crystals of α-carbonic anhydrase from T. crunogena XCL-2 have been grown and were shown to diffract X-rays to 2.6 Å resolution. The crystals belonged to space group C2, with unit-cell parameters a = 127.1, b = 102.2, c = 105.0 Å, β = 127.3°
Diffraction data were collected to a limiting resolution of 2.4 Å from a crystal of selenomethionyl-labelled SadA, an L-amino-acid dioxygenase.
YgjG is a putrescine:2-oxoglutarate aminotransferase that belongs to the class III aminotransferases. In this study, YgjG from E. coli was overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method.
The NheA component of the B. cereus Nhe toxin was overexpressed in E. coli, purified and crystallized. Diffraction data were collected and processed to 2.05 Å resolution.
Rab6A′(Q72L), a constitutively active GTP-binding form of Rab6A, was purified and crystallized. The crystals were found to belong to space group P22121, with unit-cell parameters a = 36.84, b = 96.78, c = 109.99 Å. The crystals were obtained at 293 K and diffracted to a resolution of 1.9 Å.
AIM2 is an innate immune sensor of microbial double-stranded DNA. The HIN-200 domain of mouse AIM2 bound to a 15 bp and an 18 bp dsDNA were crystallized and diffract to about 4.0 Å.
A Streptomyces homologue of the mycobacterial integration host factor mIHF was heterologously produced, purified and crystallized in the presence of a 16-mer duplex DNA by the sitting-drop vapour-diffusion method. The best crystal diffracted X-rays to 2.22 Å resolution and belonged to space group C2.
M. tuberculosis succinyl-diaminopimelate desuccinylase, the enzyme which catalyzes the seventh step of the lysine-biosynthesis pathway, has been cloned, expressed, purified and crystallized. Preliminary X-ray diffraction analysis indicated the presence of pseudo-merohedral twinning in space group P21, resulting in possible emulation of space group C2221.
Chandipura virus glycoprotein ectodomain (Gth) was purified and crystallized at pH 7.5. X-ray diffraction data set was collected to a resolution of 3.1 Å.
In order to investigate its structure and function, the medium-chain dehydrogenase/reductase superfamily YncB-like protein from V. vulnificus was expressed, purified and crystallized. X-ray diffraction analyses of YncB and the YncB–NADP(H) complex are reported at resolutions of 1.85 and 1.81 Å, respectively.
Uracil-DNA glycosylase from S. tokodaii strain 7 was overexpressed and purified. Crystals of the apo form and of a complex with uracil were obtained.
Crystals of the R. ferrooxidans SW2 iron oxidoreductase FoxE were obtained and the phase problem was solved by Fe SAD at 2.44 Å resolution.
The Vitis vinifera dual-activity fucose and nucleotide-sugar metabolizing enzyme L-fucokinase:GDP-fucose pyrophosphorylase (FKP) has been purified to homogeneity and the 118.8 kDa monomeric protein has been crystallized by vapor diffusion in Zeppezauer tubes at 277 K.
α-Phosphoglucomutase from L. lactis, a homologue of human phosphomannomutase 1, was produced and crystallized. X-ray diffraction data were collected to 1.5 Å resolution.
The cloning, expression, purification, crystallization and preliminary X-ray characterization of a trimodular type III cohesin–dockerin complex from the R. flavefaciens cellulosome system are described.
A novel reconstitution system for the modification and purification of ubiquitylated proteins yielded the first diffracting crystals of a ubiquitylated substrate, namely Rpn10.
The SFC-1 gene from S. fonticola was cloned and SFC-1 was expressed, purified and crystallized. X-ray diffraction data were collected from an SFC-1 crystal to 1.6 Å resolution.
The bacterial selenocysteine synthase SelA from Aquifex aeolicus was crystallized and the diffraction resolution was improved by lysine-residue methylation, truncation of N-terminal region (ΔN), and Lys-to-Ala point mutations. Phases were determined by using a selenomethionine-substituted crystal of the ΔN mutant.
laboratory communications
RNA polymerase from S. shibatae in complex with DNA was crystallized using a nanoseeding method. Native RNAP crystals underwent an ad hoc procedure for DNA binding; one of these crystals diffracted to 4.3 Å resolution.
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