@article{CzernetzkiArrowsmithFantuzzietal.2021, author = {Czernetzki, Corinna and Arrowsmith, Merle and Fantuzzi, Felipe and G{\"a}rtner, Annalena and Tr{\"o}ster, Tobias and Krummenacher, Ivo and Schorr, Fabian and Braunschweig, Holger}, title = {A neutral beryllium(I) radical}, series = {Angewandte Chemie International Edition}, volume = {60}, journal = {Angewandte Chemie International Edition}, number = {38}, doi = {10.1002/anie.202108405}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-256529}, pages = {20776-20780}, year = {2021}, abstract = {The reduction of a cyclic alkyl(amino)carbene (CAAC)-stabilized organoberyllium chloride yields the first neutral beryllium radical, which was characterized by EPR, IR, UV/Vis spectroscopy and X-ray crystallography. DFT calculations show significant spin density at beryllium and confirm donor-acceptor bonding between an alkylberyllium radical fragment and a neutral CAAC ligand.}, language = {en} } @article{EisenbergAlbertTeuffeletal.2022, author = {Eisenberg, Philip and Albert, Leon and Teuffel, Jonathan and Zitzow, Eric and Michaelis, Claudia and Jarick, Jane and Sehlke, Clemens and Große, Lisa and Bader, Nicole and Nunes-Alves, Ariane and Kreikemeyer, Bernd and Schindelin, Hermann and Wade, Rebecca C. and Fiedler, Tomas}, title = {The Non-phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase GapN Is a Potential New Drug Target in Streptococcus pyogenes}, series = {Frontiers in Microbiology}, volume = {13}, journal = {Frontiers in Microbiology}, issn = {1664-302X}, doi = {10.3389/fmicb.2022.802427}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-262869}, year = {2022}, abstract = {The strict human pathogen Streptococcus pyogenes causes infections of varying severity, ranging from self-limiting suppurative infections to life-threatening diseases like necrotizing fasciitis or streptococcal toxic shock syndrome. Here, we show that the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN is an essential enzyme for S. pyogenes. GapN converts glyceraldehyde 3-phosphate into 3-phosphoglycerate coupled to the reduction of NADP to NADPH. The knock-down of gapN by antisense peptide nucleic acids (asPNA) significantly reduces viable bacterial counts of S. pyogenes laboratory and macrolide-resistant clinical strains in vitro. As S. pyogenes lacks the oxidative part of the pentose phosphate pathway, GapN appears to be the major NADPH source for the bacterium. Accordingly, other streptococci that carry a complete pentose phosphate pathway are not prone to asPNA-based gapN knock-down. Determination of the crystal structure of the S. pyogenes GapN apo-enzyme revealed an unusual cis-peptide in proximity to the catalytic binding site. Furthermore, using a structural modeling approach, we correctly predicted competitive inhibition of S. pyogenes GapN by erythrose 4-phosphate, indicating that our structural model can be used for in silico screening of specific GapN inhibitors. In conclusion, the data provided here reveal that GapN is a potential target for antimicrobial substances that selectively kill S. pyogenes and other streptococci that lack the oxidative part of the pentose phosphate pathway.}, language = {en} } @article{KoelmelKuperKisker2021, author = {Koelmel, Wolfgang and Kuper, Jochen and Kisker, Caroline}, title = {Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem}, series = {Scientific Reports}, volume = {11}, journal = {Scientific Reports}, number = {1}, doi = {10.1038/s41598-021-95186-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-261644}, pages = {17038}, year = {2021}, abstract = {Over the last decades the phase problem in macromolecular x-ray crystallography has become more controllable as methods and approaches have diversified and improved. However, solving the phase problem is still one of the biggest obstacles on the way of successfully determining a crystal structure. To overcome this caveat, we have utilized the anomalous scattering properties of the heavy alkali metal cesium. We investigated the introduction of cesium in form of cesium chloride during the three major steps of protein treatment in crystallography: purification, crystallization, and cryo-protection. We derived a step-wise procedure encompassing a "quick-soak"-only approach and a combined approach of CsCl supplement during purification and cryo-protection. This procedure was successfully applied on two different proteins: (i) Lysozyme and (ii) as a proof of principle, a construct consisting of the PH domain of the TFIIH subunit p62 from Chaetomium thermophilum for de novo structure determination. Usage of CsCl thus provides a versatile, general, easy to use, and low cost phasing strategy.}, language = {en} } @article{MieczkowskiSteinmetzgerBessietal.2021, author = {Mieczkowski, Mateusz and Steinmetzger, Christian and Bessi, Irene and Lenz, Ann-Kathrin and Schmiedel, Alexander and Holzapfel, Marco and Lambert, Christoph and Pena, Vladimir and H{\"o}bartner, Claudia}, title = {Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine}, series = {Nature Communications}, volume = {12}, journal = {Nature Communications}, doi = {10.1038/s41467-021-23932-0}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-270274}, year = {2021}, abstract = {Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.}, language = {en} } @article{ScheibBroserConstantinetal.2018, author = {Scheib, Ulrike and Broser, Matthias and Constantin, Oana M. and Yang, Shang and Gao, Shiqiang and Mukherjee, Shatanik and Stehfest, Katja and Nagel, Georg and Gee, Christine E. and Hegemann, Peter}, title = {Rhodopsin-cyclases for photocontrol of cGMP/cAMP and 2.3 {\AA} structure of the adenylyl cyclase domain}, series = {Nature Communications}, volume = {9}, journal = {Nature Communications}, doi = {10.1038/s41467-018-04428-w}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-228517}, pages = {2046, 1-15}, year = {2018}, abstract = {The cyclic nucleotides cAMP and cGMP are important second messengers that orchestrate fundamental cellular responses. Here, we present the characterization of the rhodopsinguanylyl cyclase from Catenaria anguillulae (CaRhGC), which produces cGMP in response to green light with a light to dark activity ratio > 1000. After light excitation the putative signaling state forms with tau = 31 ms and decays with tau = 570 ms. Mutations (up to 6) within the nucleotide binding site generate rhodopsin-adenylyl cyclases (CaRhACs) of which the double mutated YFP-CaRhAC (E497K/C566D) is the most suitable for rapid cAMP production in neurons. Furthermore, the crystal structure of the ligand-bound AC domain (2.25 angstrom) reveals detailed information about the nucleotide binding mode within this recently discovered class of enzyme rhodopsin. Both YFP-CaRhGC and YFP-CaRhAC are favorable optogenetic tools for non-invasive, cell-selective, and spatio-temporally precise modulation of cAMP/cGMP with light.}, language = {en} } @article{TruongvanLiMisraetal.2022, author = {Truongvan, Ngoc and Li, Shurong and Misra, Mohit and Kuhn, Monika and Schindelin, Hermann}, title = {Structures of UBA6 explain its dual specificity for ubiquitin and FAT10}, series = {Nature Communications}, volume = {13}, journal = {Nature Communications}, doi = {10.1038/s41467-022-32040-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-301161}, year = {2022}, abstract = {The covalent modification of target proteins with ubiquitin or ubiquitin-like modifiers is initiated by E1 activating enzymes, which typically transfer a single modifier onto cognate conjugating enzymes. UBA6 is an unusual E1 since it activates two highly distinct modifiers, ubiquitin and FAT10. Here, we report crystal structures of UBA6 in complex with either ATP or FAT10. In the UBA6-FAT10 complex, the C-terminal domain of FAT10 binds to where ubiquitin resides in the UBA1-ubiquitin complex, however, a switch element ensures the alternate recruitment of either modifier. Simultaneously, the N-terminal domain of FAT10 interacts with the 3-helix bundle of UBA6. Site-directed mutagenesis identifies residues permitting the selective activation of either ubiquitin or FAT10. These results pave the way for studies investigating the activation of either modifier by UBA6 in physiological and pathophysiological settings.}, language = {en} }