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Thiol dioxygenases are a subset of nonheme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the nonheme iron site in 3MDO remains a matter of debate. A model for bidentate 3MPA coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrates that 3HPA and 3MPA associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O2-binding site. Supporting HYSCORE spectroscopic experiments were performed on the (3MPA/NO)-bound Av3MDO iron nitrosyl (S = 3/2) site. In combination with spectroscopic simulations and optimized DFT models, this work provides an experimentally verified model of the Av3MDO enzyme-substrate complex, effectively resolving a debate in the literature regarding the preferred substrate-binding denticity. These results elegantly explain the observed 3MDO substrate specificity, but leave unanswered questions regarding the mechanism of substrate-gated reactivity with dioxygen.

The article presents a study on the atomic resolution crystallography involving streptavidin and its biotin complex. The resolutions were conducted at 1.03 and 0.95 ampere. This study revealed that the result of the analysis of the anisotropic displacement parameters is consistent with the variation in the loop structures and the ability of the protein to bind biotin tightly is affected by the dynamic nature of the protein structure.

A detailed view is presented of the effects of one round of 20 cycles of restrained least-squares refinement of rubreythrin in which a trans peptide between Gly78 and Ile79 converts to a cis conformation automatically. While the ω angle for the peptide changes by nearly 180°, the maximum shift in any atomic position is 1.32 Å. The peptide converts by passing through a non-ideal structure containing a nearly linear C—­N—Cα bond angle. The overall motion is not possible for real or virtual molecular models with ideal bond lengths, angles and torsion angles. Strengthening the stereochemical bond length and bond angle restraints halts the structural change. [ABSTRACT FROM AUTHOR]

Reinterpretation of the space-group symmetry is reported for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase (PDB codes and ). The two structures reported in space group P1 with a dimer in the asymmetric unit can be described as C-centered monoclinic structures with one subunit in the asymmetric unit. [ABSTRACT FROM AUTHOR]

Reinterpretations of the space-group symmetry are reported for two crystal structures of phospholipase A2 isoforms (PDB codes and ). The two structures reported in space groups R3 and C2 are isomorphous with a third isoform with space group R32 (PDB code ). The original structure reports were interpreted in terms of different oligomeric forms of the isoforms, but these conclusions are not supported by the isomorphous structures. [ABSTRACT FROM AUTHOR]

The structure of a full-length streptavidin has been determined at 1.7Å resolution and shows that the 20 residue extension at the C terminus forms a well-ordered polypeptide loop on the surface of the tetramer. Residues 150–153 of the extension are bound to the ligand-binding site, possibly competing with exogenous ligands. The binding mode of these residues is compared with that of biotin and peptidic ligands. The observed structure helps to rationalize the observations that full-length mature streptavidin binds biotinylated macromolecules with reduced affinity. [Copyright &y& Elsevier]