D-Alanine-D-alanine ligase (DDL) catalyzes the biosynthesis of d-alanyl-d-alanine, an essential bacterial peptidoglycan precursor, and is an important drug target for the development of antibacterials. We determined four different crystal structures of DDL from Xanthomonas oryzae pv. oryzae (Xoo) causing Bacteria Blight (BB), which include apo, ADP-bound, ATP-bound, and AMPPNP-bound structures at the resolution between 2.3 and 2.0 Å. Similarly with other DDLs, the active site of XoDDL is formed by three loops from three domains at the center of enzyme. Compared with d-alanyl-d-alanine and ATP-bound TtDDL structure, the γ-phosphate of ATP in XoDDL structure was shifted outside toward solution. We swapped the ω-loop (loop3) of XoDDL with those of Escherichia coli and Helicobacter pylori DDLs, and measured the enzymatic kinetics of wild-type XoDDL and two mutant XoDDLs with the swapped ω-loops. Results showed that the direct interactions between ω-loop and other two loops are essential for the active ATP conformation for D-ala-phosphate formation.
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http://dx.doi.org/10.1016/j.abb.2014.01.009 | DOI Listing |
Phys Rev Lett
December 2024
School of Physics, Beihang University, Haidian District, Beijing 100191, China.
Massive Dirac fermions, which are essential for realizing novel topological phenomena, are expected to be generated from massless Dirac fermions by breaking the related symmetry, such as time-reversal symmetry in topological insulators or crystal symmetry in topological crystalline insulators. Here, we report scanning tunneling microscopy and angle-resolved photoemission spectroscopy studies of α-Bi_{4}I_{4}, which reveals the realization of massive Dirac fermions in the (100) surface states without breaking the time-reversal symmetry. Combined with first-principles calculations, our experimental results indicate that the spontaneous symmetry breaking engenders two nondegenerate edge states at the opposite sides of monolayer Bi_{4}I_{4} after the structural phase transition, imparting mass to the Dirac fermions after taking the interlayer coupling into account.
View Article and Find Full Text PDFPhys Rev Lett
December 2024
Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada.
Based on its simple valence electron configuration, we may expect lithium to have straightforward physical properties that are easily explained. However, solid lithium, when cooled below 77 K, develops a complex structure that has been debated for decades. A close parallel is found in sodium below 36 K where the crystal structure still remains unresolved.
View Article and Find Full Text PDFInorg Chem
January 2025
Department of Material Science and Engineering, NTNU Norwegian University of Science and Technology, Trondheim 7491, Norway.
The chemical flexibility of the tetragonal tungsten bronze (TTB) structure offers a large potential for compositional engineering. Cation size and vacancy concentration are known to affect its structure, cation disorder, and functional properties. However, the compositional complexity also makes the TTB structure challenging to understand.
View Article and Find Full Text PDFInorg Chem
January 2025
Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States.
The supramolecular binding exclusively by H-bonds of SeO, MoO and WO ions to form nanojars of the formula [EO⊂{-Cu(μ-OH)(μ-pz)}] (; E = Se, Mo, W; = 28-34; pz = pyrazolate) was studied in solution by electrospray ionization mass spectrometry, variable temperature, paramagnetic H NMR and UV-vis spectroscopy, and in the solid state by single-crystal X-ray crystallography. These large anions allow for the observation of a record nanojar size, (E = Mo, W). Six crystal structures are described of nanojars of varying sizes with either SeO, MoO or WO entrapped ions, including the first example of a cocrystal of two different nanojars in crystallographically unique positions, and .
View Article and Find Full Text PDFAngew Chem Int Ed Engl
January 2025
Darmstadt University of Technology: Technische Universitat Darmstadt, Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, Alarich-Weiss-Strasse 4, 64287, Darmstadt, GERMANY.
Macrocycles are increasingly considered as promising modalities to target challenging intracellular proteins. However, strategies for transitioning from active linear starting points to improved macrocycles are still underdeveloped. Here we explored the derivatization of linkers as an approach for macrocycle optimization.
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