Diffraction structural biology – an introductory overview

Introducing the special issue on diffraction structural biology available at https://journals.iucr.org/special_issues/2021/ISDSB2019.

Structure and comparison of the motor domain of centromere-associated protein E

Crystallization and structure determination of the motor domain of centromere-associated protein E in complex with its inhibitor was performed. In the determined structure, endogenous ADP was observed in the nucleotide-binding site instead of the inhibitor.

Recent structural insights into the mechanism of lysozyme hydrolysis

The complex of lysozyme with an N-acetylglucosamine tetramer shows a relatively strong hydrogen-bond network around a catalytic residue via high-resolution X-ray structural analysis. This indicates a potentially different hydrolysis mechanism to that through a glycosyl intermediate, and this is expected to be proved using neutron experiments.

Structure of macrophage migration inhibitory factor in complex with methotrexate

Structure determination of the complex of macrophage migration inhibitory factor (MIF) with methotrexate (MTX) and fragment molecular-orbital calculations quantified the interaction between MTX and MIF and revealed the amino acids that are effective in the interaction of MTX and MIF.

Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method

A new room-temperature (RT) data-collection method for microcrystals was developed by combining serial synchrotron rotation crystallography with the humid air and glue-coating method. The RT data-collection strategy for micro-crystallography was evaluated by examining the efficiency, the influence of non-isomorphism and radiation damage, and the effectiveness of increasing the number of merged images. An equation was proposed that relates the achievable resolution to the total photon flux used to obtain a data set.

Macromolecular crystallography using microcrystal electron diffraction

The current status and ongoing development of 3D electron diffraction and microcrystal electron diffraction in macromolecular crystallography are reviewed.

Crystal structures of adenylylated and unadenylylated P_II protein GlnK from Corynebacterium glutamicum

The crystal structures of adenylylated and unadenylylated GlnK, a P_II protein from Corynebacterium glutamicum, indicate that adenylylation of Tyr51 in the T-loop does not interfere with the P_II-typical conformational changes that occur in the T-loop upon effector binding. Rather, T-loop adenylylation further expands the repertoire of mechanisms that enable P_II function.

Structural insights into the substrate-binding cleft of AlyF reveal the first long-chain alginate-binding mode

The structure of the alginate lyase AlyF in complex with the long alginate oligosaccharide G6 revealed the whole substrate-binding cleft and the role of three flexible loops involved in substrate binding. Accordingly, a long-chain substrate-binding model was proposed for AlyF.

The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2

DpaA from P. agarilytica NO2, a novel type of haloalkane dehalogenase, was successfully purified and crystallized. The model of DpaA based on the crystallographic data reported here provides the first example of a tetrameric structure in haloalkane dehalogenase subfamily I.

Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase

To discover a different conformation of the phosphohistidine loop in succinyl-CoA synthetase (SCS), the GTP-specific SCS was co-crystallized with Mg²⁺-GDP and with Mg²⁺-GMPPNP and Mg²⁺-GMPPCP, which are nonhydrolysable analogues of Mg²⁺-GTP. In addition, phosphorylated GTP-specific SCS was co-crystallized with Mg²⁺-succinate and desulfo-CoA. The phosphohistidine loop was observed with the active-site histidine residue in the nucleotide-binding site, and a second succinate-binding site was revealed.

Structure and functional properties of the cold-adapted catalase from Acinetobacter sp. Ver3 native to the Atacama plateau in northern Argentina

Biochemical and structural features of the cold-adapted Acinetobacter sp. Ver3 catalase KatE1 are reported.

Characterization of the sorbitol de­hydrogenase SmoS from Sinorhizobium meliloti 1021

The sorbitol dehydrogenase SmoS from S. meliloti crystallized as a tetramer and showed activity using sorbitol or galactitol as a substrate while exhibiting a preference for sorbitol. Substrate binding was modelled and the total energy difference between bound and unbound complexes was calculated.