Isopenicillin synthase (IPNS) catalyzes the unique reaction of l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.
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http://dx.doi.org/10.1126/sciadv.abh0250 | DOI Listing |
Sci Adv
January 2025
Laboratoire de Physique des Solides, Université Paris-Saclay, CNRS, 91405 Orsay, France.
Charge transport in materials has an impact on a wide range of devices based on semiconductor, battery, or superconductor technology. Charge transport in sliding charge density waves (CDW) differs from all others in that the atomic lattice is directly involved in the transport process. To obtain an overall picture of the structural changes associated to the collective transport, the large coherent x-ray beam generated by an x-ray free-electron laser (XFEL) source was used.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China.
Subcell Biochem
December 2024
ALBA Synchrotron Light Source, Cerdanyola del Vallès, Spain.
Since the 1970s and for about 40 years, X-ray crystallography has been by far the most powerful approach for determining virus structures at close to atomic resolutions. Information provided by these studies has deeply and extensively enriched and shaped our vision of the virus world. In turn, the ever-increasing complexity and size of the virus structures being investigated have constituted a major driving force for methodological and conceptual developments in X-ray macromolecular crystallography (MX).
View Article and Find Full Text PDFSci Rep
December 2024
Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Kyungbook, Republic of Korea.
Alanine racemase (Alr) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent racemization between L- and D-alanine in bacteria. Owing to the potential interest in targeting Alr for antibacterial drug development, several studies have determined the structures of Alr from different species, proposing models for the reaction mechanism. Insights into its reaction dynamics may be conducive to a better understanding of the Alr reaction mechanism.
View Article and Find Full Text PDFWe theoretically investigate the impact of nonlinear dispersion of crystals and multilayers used in Laue-type pulse compressors (LPCs) on chirped x-ray pulse compression, as well as the optimization method for the configuration of LPCs. We also study the application of LPCs to compress chirped x-ray free-electron laser pulses based on the parameters of LCLS-II-HE. The results show that the optimal thickness is half of the Pendellosung period, yielding the best compressor performance with minimal impact from the nonlinear dispersion.
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