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Czech National Centre of the European Research Infrastructure Consortium INSTRUCT ERIC

A gateway to realm of structural data for biochemists, biophysicists, molecular biologist, and all scientists whose research benefits from accurate structure determination of biological macromolecules, assemblies, and complex molecular machineries at atomic resolution.

Open access to 10 high-end core facilities and assisted expertise in NMR, X-ray crystallography and crystallization, cryo-electron microscopy and tomography, biophysical characterization of biomolecular interaction, nanobiotechnology, proteomics and structural mass spectrometry.

A distributed infrastructure constituted by Core Facilities of CEITEC (Central European Institute of Technology), located in Brno, and BIOCEV (Biotechnology and Biomedicine Centre), located in Vestec near Prague, Central Bohemia.

Research Highlights

the best of science obtained using CIISB Core Facilities

J. Am. Chem. Soc. 2020

Nature Index Journal

Crystal structures of (A) PBD anthramycin covalently bound to DNA strands and (B) lincomycin targeting the peptidyl transferase center in the 50S ribosomal subunit of Staphylococcus aureus.

Jiří Janata Research Group

Significance

Antitumor pyrrolobenzodiazepines (PBDs), lincosamide antibiotics, quorumsensing molecule hormaomycin, and antimicrobial griselimycin are structurally and functionally diverse groups of actinobacterial metabolites. The common feature of these compounds is the incorporation of L -tyrosine- or L -leucine-derived 4-alkyl-L -proline derivatives (APDs) in their structures. In this study, the authors report that the last reaction in the biosynthetic pathway of APDs, catalyzed by F420 H2 -dependent Apd6 reductases, contributes to the structural diversity of APD precursors. Specifically, the heterologous overproduction of six Apd6 enzymes demonstrated that Apd6 from the biosynthesis of PBDs and hormaomycin can reduce only an endocyclic imine double bond, whereas Apd6 LmbY and partially GriH from the biosynthesis of lincomycin and griselimycin, respectively, also reduce the more inert exocyclic double bond of the same 4- substituted Δ 1-pyrroline-2-carboxylic acid substrate, making LmbY and GriH unusual, if not unique, among reductases. Furthermore, the differences in the reaction specificity of the Apd6 reductases determine the formation of the fully saturated APD moiety of lincomycin versus the unsaturated APD moiety of PBDs, providing molecules with optimal shapes to bind their distinct biological targets. Moreover, the Apd6 reductases establish the first F420 H2-dependent enzymes from the luciferase-like hydride transferase protein superfamily in the biosynthesis of bioactive molecules. Finally, bioinformatics analysis demonstrates that Apd6 and their homologues, widely distributed within several bacterial phyla, play a role in the formation of novel yet unknown natural products with incorporated L-proline-like precursors and likely in the microbial central metabolism.

Steiningerova, L. Kamenik, Z.*,  Gazak, R.,  Kadlcik, S.,  Bashiri, G.,  Man, P., Kuzma, M., Pavlikova, M., and Janata, J.: Different Reaction Specificities of F420H2Dependent Reductases Facilitate Pyrrolobenzodiazepines and Lincomycin To Fit Their Biological Targets, J. Am. Chem. Soc.  2020, 142, 3440-3448, https://dx.doi.org/10.1021/jacs.9b11234

 

Nature Communications 2020

Nature Index Journal

Cryo-EM structure of pT=4 quasi-icosahedral BDP and its penatameric and hexameric components. a Surface model of pT = 4 quasi-icosahedral BDP particle, displayed on the left side. A ribbon model of a cmcD pentamer and three cmcC′ hexamers is displayed on the right side. Pentameric cmcD protein is colored in yellow and hexameric cmcC′ is colored in green. Note that the fivefold symmetry axis is located at the center of cmcD pentamer and threefold axis is located in the middle between three cmcC′ hexamers. b Electrostatic surface potential of pentameric cmcD and hexameric cmcC′. Note the pores in the centers of pentamers and hexamers.

Kaspas Tars Research Group

Significance

Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.

Kalnins, G., Cesle, E-E., Jansons, J., Liepins, J., Filimonenko, A., and Tars, K.: Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles, Nature Comm. (2020) 11 (1), No. 388, doi.org/10.1038/s41467-019-14205-y

 

 

 

 

More publications Research Highlights archive

Reader’s Corner

literature to read, science to follow

In this section, a distinct selection of six highly stimulating research publications and reviews published during past 6 months is presented. It is our hope that links to exciting science, which deserves attention of the structural biology community, will help you to locate gems in the steadily expanding jungle of scientific literature. You are welcome to point out to any paper you found interesting by sending a link or citation to readerscorner@ciisb.org. The section is being updated regularly.


 

Reader’s Corner Archive

Quote of March

“The mediocre teacher tells. The good teacher explains. The superior teacher demonstrates. The great teacher inspires.”

William Arthur Ward