Cryo-neutron crystallographic data collection and preliminary refinement of left-handed Z-DNA d(CGCGCG)

The first cryo-neutron diffraction experiment for a DNA oligonucleotide crystal is reported. Data collection in less than two days with a crystal of approximate size 0.25 mm³ yielded a data set of >90% completeness to a resolution of 1.7 Å.

Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate de­hydrogenase

Crystal structures of apo malate dehydrogenase (MDH) from Methylobacterium extorquens, MDH bound to NAD⁺, and MDH with oxaloacetate and ADP-ribose revealed conformational changes, closing the active site upon coenzyme and substrate binding. In the ternary complex, His284 is in position to donate a proton in the formation of (2S)-malate.

Structure of glyoxysomal malate de­hydrogenase (MDH3) from Saccharomyces cerevisiae

The crystal structure of glyoxysomal malate dehydrogenase (MDH3) from Saccharomyces cerevisiae was determined at 2.1 Å resolution in complex with NAD⁺ and oxaloacetate. The structure of the active-site loop in MDH3 differed from those of mitochondrial and cytosolic malate dehydrogenases.

Crystal structure of Arabidopsis thaliana peroxiredoxin A C119S mutant

Peroxiredoxin A (PrxA) from Arabidopsis thaliana chloroplasts belongs to the 2-Cys Prx family. The crystal structure of a PrxA C119S mutant at 2.6 Å resolution shows the protein exists as a decamer, which was corroborated in solution. The structure is in the reduced state, suitable for the approach of peroxide.

Crystal structure of the ribonuclease-P-protein subunit from Staphylococcus aureus

Staphylococcus aureus ribonuclease-P-protein subunit (RnpA) is a promising antimicrobial target. The crystal structure of RnpA at 2.0 Å resolution shows key similarities with RnpA structures from bacteria and archaea and will be instrumental in designing inhibitors targeting RnpA-mediated RNA processing.

Crystal structure of mutant carboxypeptidase T from Thermoactinomyces vulgaris with an implanted S1′ subsite from pancreatic carboxypeptidase B

A mutant of carboxypeptidase T (CPT) has been generated in which the amino-acids of the S1′ subsite are substituted by the corresponding residues from pancreatic carboxypeptidase B (CPB). The mutant enzyme retained the broad selectivity of wild-type CPT. A comparison of the structures of CPT, the mutant and CPB showed that the S1′ subsite has not been distorted by the mutagenesis and adequately reproduces the structure of the CPB S1′ subsite, but differs from CPB in substrate selectivity.

The novel metallo-β-lactamase PNGM-1 from a deep-sea sediment metagenome: crystallization and X-ray crystallographic analysis

Metallo-β-lactamases (MBLs) may hydrolyze the β-lactam rings of antibiotics. PNGM-1 is a subclass B3 deep-sea sediment MBL that predates the antibiotic era. Crystals of native and selenomethionine-substituted PNGM-1 diffracted to 2.1 and 2.3 Å resolution, respectively. They belonged to space group P2₁ and probably contain 6–10 molecules in the crystallographic asymmetric unit.

Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine

X-ray crystal structures of superfolder green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine (pNO₂F) independently incorporated at two sites in the protein are reported. These structures support the use of pNO₂F as a relatively nonperturbative spectroscopic reporter of local protein environment.

Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence

X-ray structures of the ETSi domain of human ERG3 and of its complex with the E74 promoter DNA sequence are reported. Comparison of the ETSi–DNA₉ structure with known structures of ETS class 1 protein–DNA complexes shows the similarities and differences in the promoter DNA binding and specificity of the class 1 ETS proteins.

Re-refinement of Plasmodium falciparum orotidine 5′-monophosphate de­carboxylase provides a clearer picture of an important malarial drug target

In order to facilitate structure-based drug-design efforts, a set of structures of orotidine 5′-monophosphate decarboxylase from the malaria parasite P. falciparum were re-refined. This refitting greatly improves the global statistics of all three structures and shows that adding the substrate orotidine 5′-monophosphate to the enzyme (PDB entry 2za1) generates a complex with the product UMP, rather than the substrate OMP as initially interpreted.

X-ray structure of Arthrobacter globiformis M30 ketose 3-epimerase for the production of D-allulose from D-fructose

The crystal structure of A. globiformis M30 ketose 3-epimerase was determined at 1.96 Å resolution.

Redox manipulation of the manganese metal in human manganese superoxide dismutase for neutron diffraction

Human mitochondrial manganese superoxide dismutase (MnSOD) is a major player in combating reactive oxygen species in the human body. Methods have been found to control the redox state of the active-site metal of large perdeuterated MnSOD crystals. Neutron diffraction data from these crystals were collected to study the effect of the redox state on proton location. These methods can be applied to other crystal systems where information on the location of protons in specific chemical states is needed.