Chen Wei-Hung, Li Kunhua, Guntaka Naga Sandhya, Bruner Steven D
Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States.
ACS Chem Biol. 2016 Aug 19;11(8):2293-303. doi: 10.1021/acschembio.6b00332. Epub 2016 Jun 24.
Nonribosomal peptide synthetases are large, complex multidomain enzymes responsible for the biosynthesis of a wide range of peptidic natural products. Inherent to synthetase chemistry is the thioester templated mechanism that relies on protein/protein interactions and interdomain dynamics. Several questions related to structure and mechanism remain to be addressed, including the incorporation of accessory domains and intermodule interactions. The inclusion of nonproteinogenic d-amino acids into peptide frameworks is a common and important modification for bioactive nonribosomal peptides. Epimerization domains, embedded in nonribosomal peptide synthetases assembly lines, catalyze the l- to d-amino acid conversion. Here we report the structure of the epimerization domain/peptidyl carrier protein didomain construct from the first module of the cyclic peptide antibiotic gramicidin synthetase. Both holo (phosphopantethiene post-translationally modified) and apo structures were determined, each representing catalytically relevant conformations of the two domains. The structures provide insight into domain-domain recognition, substrate delivery during the assembly line process, in addition to the structural organization of homologous condensation domains, canonical players in all synthetase modules.
非核糖体肽合成酶是一类大型、复杂的多结构域酶，负责多种肽类天然产物的生物合成。合成酶化学的固有特征是硫酯模板机制，该机制依赖于蛋白质/蛋白质相互作用和结构域间的动力学。几个与结构和机制相关的问题仍有待解决，包括辅助结构域的并入和模块间相互作用。将非蛋白质ogenic d-氨基酸纳入肽骨架是生物活性非核糖体肽常见且重要的修饰。嵌入非核糖体肽合成酶装配线中的差向异构化结构域催化 l-氨基酸向 d-氨基酸的转化。在此，我们报道了来自环肽抗生素短杆菌肽合成酶第一个模块的差向异构化结构域/肽基载体蛋白双结构域构建体的结构。确定了全酶（翻译后经磷酸泛酰巯基乙胺修饰）和脱辅基结构，每个结构都代表了这两个结构域的催化相关构象。这些结构除了揭示同源缩合结构域（所有合成酶模块中的典型成分）的结构组织外，还为结构域-结构域识别以及装配线过程中的底物传递提供了深入了解。
