Acta Crystallographica Section F
Section F STRUCTURAL BIOLOGY COMMUNICATIONS
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Volume 74| Part 11
Cover illustration: A llama-derived nanobody targeting the J-base binding protein 1 [van Beusekom et al. (2018), Acta Cryst. F74, 690-695]. J-base binding protein 1 contributes to the biosynthesis and maintenance of base J, a modification of thymidine confined to some protozoa.
Acta Cryst. (2018). F74, 688-689
https://doi.org/10.1107/S2053230X18015340
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Characterization and structure determination of a llama-derived nanobody targeting the J-base binding protein 1
B. van Beusekom, T. Heidebrecht, A. Adamopoulos, A. Fish, E. Pardon, J. Steyaert, R. P. Joosten and A. Perrakis
A camelid single-domain antibody fragment (nanobody) is shown to have high affinity towards its recognition target, the J-base binding protein 1. The serendipitous crystallization of this nanobody alone, solution of its crystal structure and its refinement to 1.64 Å resolution are described. Ensemble refinement suggests that in the ligand-free state one of the complementarity-determining regions (CDRs) is flexible, while the other two adopt well defined conformations.
PDB reference: Nb6, 6fpv
Crystallization of ectonucleotide phosphodiesterase/pyrophosphatase-3 and orientation of the SMB domains in the full-length ectodomain
C. Döhler, M. Zebisch, D. Krinke, A. Robitzki and N. Sträter
Well diffracting crystals of the ectodomain of rat ectonucleotide phosphodiesterase/pyrophosphatase-3 were obtained for a construct lacking the SMB domains, while the structure of the full-length ectodomain reveals the orientation of the SMB domains but has a partially disordered active-site structure, probably owing to the absence of the active-site zinc ions.
PDB reference: ectonucleotide phosphodiesterase/pyrophosphatase-3, 6g4g
https://doi.org/10.1107/S2053230X1801292X
Crystal structures of the N-terminal domain of the Staphylococcus aureus DEAD-box RNA helicase CshA and its complex with AMP
X. Chen, C. Wang, X. Zhang, T. Tian and J. Zang
Crystal structures of the RecA-like domain 1 of Staphylococcus aureus CshA (SaCshA) and of its complex with AMP are reported; SaCshA shares a highly conserved ATP-binding mechanism with other DEAD-box RNA helicases.
PDB references: N-terminal domain of CshA, 6aib; complex with AMP, 6aic
BpeB, a major resistance-nodulation-cell division transporter from Burkholderia cenocepacia: construct design, crystallization and preliminary structural analysis
T. Horikawa, L.-W. Hung, H.-B. Kim, D. Shaya, C.-Y. Kim, T. C. Terwilliger, E. Yamashita, M. Aoki, U. Okada and S. Murakami
BpeB, which is a major multidrug-efflux transporter in Burkholderia cenocepacia, has a C-terminal region that extends beyond those of other homologous resistance-nodulation-cell division transporters such as AcrB and MexB. Comparative modeling helped to identify truncation variants that could aid the crystallization of BpeB without eliminating its molecular functions.
High-resolution structures of inhibitor complexes of human indole­amine 2,3-dioxygenase 1 in a new crystal form
S. Luo, K. Xu, S. Xiang, J. Chen, C. Chen, C. Guo, Y. Tong and L. Tong
Human indoleamine 2,3-dioxygenase 1 (IDO1) is a potential target for drug discovery. Three new crystal forms of human IDO1 are reported, obtained by introducing a double mutation on the surface. One of these crystal forms can diffract to high resolution and can be readily used for soaking experiments with inhibitors. This mutant represents a robust platform for determining structures of IDO1 inhibitor and substrate complexes at high resolution.
PDB references: indoleamine 2,3-dioxygenase 1, complex with epacadostat, 6e40; complex with sulfur analog of epacadostat, 6e41; complex with 4-chlorophenyl imidazole, 6e42; complex with anolog of BMS-978587, 6e43; free enzyme (ferric), 6e44; free enzyme (ferrous), 6e45; complex with tryptophan (ferrous), 6e46
Crystal structures and kinetics of N-acetylneuraminate lyase from Fusobacterium nucleatum
J. P. Kumar, H. Rao, V. Nayak and S. Ramaswamy
Structures of N-acetyl-D-neuraminic acid lyase in the ligand-free form and of a covalent Schiff base adduct are reported. The structure and kinetic data reveal the conserved nature of these proteins among Gram-negative bacteria.
PDB references: N-acetylneuraminate lyase from F. nucleatum, 5zjm; pyruvate Schiff-base intermediate, 5zka
Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA de­hydrogenase from Clostridium aceto­butylicum
M. Takenoya, S. Taguchi and S. Yajima
Crystal structures of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum have been determined in apo and NAD+-bound forms. The structures, together with kinetic analyses using single-amino-acid substituted mutants, revealed the catalytically important residues in the enzyme.
PDB references: (S)-3-hydroxybutyryl-CoA dehydrogenase from C. acetobutylicum, apo form, 6acq; NAD+-bound form, 6aa8
Crystal structure of glycosyltrehalose synthase from Sulfolobus shibatae DSM5389
N. Okazaki, M. Blaber, R. Kuroki and T. Tamada
Glycosyltrehalose synthase from Sulfolobus shibatae DSM5389 has an optimum catalytic cavity for the intramolecular transglycosylation mechanism in the first step of the biosynthesis of trehalose, which converts the glucosidic bond between the last two glucose residues of amylose from an α-1,4 bond to an α-1,1 bond.
PDB reference: glycosyltrehalose synthase, 5zcr
Combining crystallogenesis methods to produce diffraction-quality crystals of a psychrophilic tRNA-maturation enzyme
R. de Wijn, O. Hennig, F. G. M. Ernst, B. Lorber, H. Betat, M. Mörl and C. Sauter
Advanced crystallogenesis methods, including microseed matrix screening, crystallization optimization by counter-diffusion and crystal detection by trace fluorescent labeling, were used in combination to successfully produce various diffracting crystal forms of a CCA-adding enzyme from the psychrophilic bacterium Planococcus halocryophilus.
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