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May 2014 issue
Cover illustration: Structure of the first sugar-binding protein from a phytopathogenic bacterium, highly conserved in the Xanthomonas genus (Medrano et al., p. 564).
IYCr crystallization series
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This article highlights some of the ground-based studies emanating from NASA's Microgravity Protein Crystal Growth (PCG) program, and includes a more detailed discussion of the history and the progress made in one of the NASA-funded PCG investigations involving the use of measured second virial coefficients (B values) as a diagnostic indicator of solution conditions conducive to protein crystallization.
The crystal structure at 3.0 Å resolution of TOP2 oligopeptidase from A. thaliana is reported.
PDB reference: TOP2 oligopeptidase, 4put
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The crystal structure of E. coli catabolite activator protein with bound cobalt(II) and sulfate ions at 1.97 Å resolution is reported.
PDB reference: catabolite activator protein, 4ft8
Structure of the first sugar-binding protein from a phytopathogenic bacterium, highly conserved in Xanthomonas genus.
PDB reference: Xac-MalE, 3uor
The 1.60 Å resolution crystal structure of the aldo-keto reductase Rv2971, an isoniazid drug target in M. tuberculosis, reveals unique characteristics of the isoniazid–NADPH binding pocket.
PDB reference: Rv2971, 4otk
Wild-type human muscle Pfk was crystallized in space group P6222. Molecular replacement with the rabbit muscle homologue shows that a dimer of the physiological tetramer is present in the crystals.
PDB reference: human muscle phosphofructokinase, 4omt
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The structure of the tyrosine aminotransferase from the parasitic protozoa L. infantum was solved to 2.35 Å resolution. The difference in substrate specificity and enzymatic activity between leishmanial and mammalian TAT is explained based on the presence of two residues (Gln55 and Asn58).
PDB reference: tyrosine aminotransferase, 4ix8
A reductive methylation-modified RRF from Thermoanaerobacter tengcongensis (TteRRF) has been crystallized using the vapour-diffusion method. The crystal belonged to space group P6122/P6522 with unit-cell parameters a = b = 103.26, c = 89.17 Å.
A ternary complex of cardiac transcription factors, NKX2.5 and TBX5, and their target DNA was crystallized, and diffraction data were collected to a resolution of 2.88 Å.
The cytoplasmic domain of the human mitochondiral dynamics protein MiD51 was expressed, purified and crystallized and a diffraction data set was collected to a resolution of 3.1 Å.
Staphylococcal superantigen-like protein 1 (SSL1) was cloned, purified and crystallized. X-ray diffraction data were collected from an SSL1 crystal to 2.5 Å resolution.
The XoGroEL gene (XOO_4288) was cloned from X. oryzae pv. oryzae and the protein was expressed, purified and crystallized. A preliminary X-ray crystallographic analysis of an XoGroEL crystal was performed.
The recombinant dephospho-CoA kinase from Legionella pneumophila was overexpressed, purified and crystallized to 2.10 Å, and its structure has been determined by molecular replacement.
The N-terminal domain of the 26S proteasome regulatory subunit p27 and its complex with the ATPase domain of Rpt5 from Mus musculus were crystallized, yielding crystals diffracting 1.7 and 4.0 Å, respectively.
A truncated family 43 glycoside hydrolase module (CtGH43) from C. thermocellum ATCC 27405 was purified and crystallized. Data were collected to 1.1 and 1.65 Å resolution in monoclinic and cubic space groups, respectively.
The SKICH domain of human TAX1BP1 was successfully expressed in E. coli, purified and crystallized. The crystal diffracted to a resolution of 1.9 Å. A molecular-replacement solution was found using the structure of the SKICH domain of NDP52 as a search model.
PigI, a key enzyme in the biosynthesis of prodigiosin, catalyzes the first step by converting L-proline to L-prolyl-AMP. Here the crystallization and preliminary crystallographic analysis of PigI is reported.
The N-terminal domain of the flagellar pocket collar protein BILBO1 from T. brucei was cloned, overexpressed, purified and crystallized. Anomalous X-ray diffraction data were collected to 1.7 Å resolution.
GatD, one of the proteins involved in the amidation of glutamic acid residues of S. aureus peptidoglycan, was crystallized and data were collected from both native and SeMet-derivatized crystals.
The β-L-arabinofuranosidase (HypBA1) from Bifidobacterium longum has been expressed in Escherichia coli and the purified recombinant protein crystallized.
The TON-0309 gene encoding DNA-directed RNA polymerase subunit L (ToRNAP_L) from T. onnurineus NA1 was cloned and the protein was expressed in E. coli, purified and crystallized. A preliminary X-ray crystallographic analysis of a ToRNAP_L crystal was performed.
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of N-acetylmannosamine kinase from methicillin-resistant S. aureus, a novel antibiotic target within sialic acid catabolism, are reported.
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis to 1.84 Å resolution of N-acetylmannosamine-6-phosphate 2-epimerase from methicillin-resistant S. aureus, an enzyme involved in the catabolism of sialic acid and a novel antimicrobial drug target, are reported.
A ScaA X-dockerin derivative with an engineered restricted single binding mode complexed with the third ScaB cohesin from A. cellulolyticus has been crystallized and data were collected to a resolution of 2.41 Å.
Crystals of the DR1998 catalase from the radiation-resistant bacterium D. radiodurans have been produced. The purification of the protein from the native source, its crystallization and preliminary X-ray crystallographic analysis are reported.
Diaminopimelate decarboxylase catalyses the last step in lysine biosynthesis: the decarboxylation of meso-diaminopimelate to form the essential amino acid S-lysine. Here, the crystallization of the two putative diaminopimelate decarboxylase isoforms from Arabidopsis thaliana, DapDc1 and DapDc2, are reported; the crystals diffracted to beyond 2.00 and 2.27 Å resolution, respectively.
Manganese superoxide dismutase (MnSOD) from A. thaliana was expressed, purified and crystallized. An X-ray diffraction data set was collected to a resolution of 1.95 Å.
The tripartite motif-containing protein 2 (TRIM2) functions as an E3 ubiquitin ligase. The crystal structure of the NHL domain of TRIM2, which belonged to space group P21, with unit-cell parameters a = 43.6, b = 76.4, c = 107.4 Å, α = 90.0, β = 94.0 and γ = 90.0° has been determined.
The SAM-dependent methyltransferase EgtD, an enzyme involved in ergothioneine biosynthesis, has been crystallized and native data have been collected as well as anomalous diffraction data at the K edge of a crystal of seleno-L-methionine-labelled protein.
A novel sample mount for use in macromolecular neutron and X-ray crystallography is described.
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