issue contents
March 2021 issue
ISDSB2019
Free
Introducing the special issue on diffraction structural biology available at https://journals.iucr.org/special_issues/2021/ISDSB2019.
Open access
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.
PDB reference: CENP-E motor domain, 6m4i
Open access
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 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.
PDB reference: MIF–MTX complex, 5xej
Open access
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.
CCP-EM
Open access
The current status and ongoing development of 3D electron diffraction and microcrystal electron diffraction in macromolecular crystallography are reviewed.
research papers
Open access
The crystal structures of adenylylated and unadenylylated GlnK, a PII protein from Corynebacterium glutamicum, indicate that adenylylation of Tyr51 in the T-loop does not interfere with the PII-typical conformational changes that occur in the T-loop upon effector binding. Rather, T-loop adenylylation further expands the repertoire of mechanisms that enable PII function.
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.
PDB reference: AlyF, complex with G6, 7bz0
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.
PDB reference: DpaA from P. agarilytica NO2, 7avr
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.
Biochemical and structural features of the cold-adapted Acinetobacter sp. Ver3 catalase KatE1 are reported.
PDB reference: KatE1 from Acinetobacter sp. Ver3, 6pt7
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.