title: Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited.
abstract: The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.
authors.affiliation: University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia.
authors.forename: Roman
authors.initials: R
authors.lastname: Šink
authors.affiliation: Lek Pharmaceuticals d. d., Verovškova 57, Ljubljana, Slovenia.
authors.forename: Miha
authors.initials: M
authors.lastname: Kotnik
authors.affiliation: University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia.
authors.forename: Anamarija
authors.initials: A
authors.lastname: Zega
authors.affiliation: Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Barreteau
authors.affiliation: University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia.
authors.forename: Stanislav
authors.initials: S
authors.lastname: Gobec
authors.affiliation: Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Blanot
authors.affiliation: Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France.|CNRS, IBS, Grenoble, France.|CEA, IBS, Grenoble, France.|Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil.
authors.forename: Andréa
authors.initials: A
authors.lastname: Dessen
authors.affiliation: Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France.|CNRS, IBS, Grenoble, France.|CEA, IBS, Grenoble, France.
authors.forename: Carlos
authors.initials: C
authors.lastname: Contreras-Martel
mesh_terms: D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology*; D010453:Peptide Synthases / Q000737:chemistry* / Q000378:metabolism; D010457:Peptidoglycan / Q000096:biosynthesis / Q000737:chemistry; D017434:Protein Structure, Tertiary
chemical_list: D010457:Peptidoglycan; D010453:Peptide Synthases; C053379:UDP-N-acetylmuramoylalanine-D-glutamate ligase