9CEN

Structure of the thiocysteine lyase (SH) domain from guangnanmycin A biosynthetic pathway

Summary for 9CEN

• Entry DOI: 10.2210/pdb9cen/pdb
• Descriptor: Polyketide Synthase Protein, POTASSIUM ION, ACETATE ION, ... (4 entities in total)
• Functional Keywords: thiocysteine lyase, polyketide synthase, natural product, sulfur incorporation., biosynthetic protein
• Biological source: Streptomyces sp. CB01883
• Total number of polymer chains: 2
• Total formula weight: 99574.12

Authors

Li, G.,Chang, C.,Shen, B. (deposition date: 2024-06-26, release date: 2024-09-25, Last modification date: 2024-12-11)

Primary citation

Steele, A.D.,Meng, S.,Li, G.,Kalkreuter, E.,Chang, C.,Shen, B.
Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain.
J.Am.Chem.Soc., 146:32605-32617, 2024

PubMed Abstract: Polyketide synthases (PKSs) are renowned for the structural diversity of the polyketide natural products they produce, but sulfur-containing functionalities are rarely installed by PKSs. We previously characterized thiocysteine lyase (SH) domains involved in the biosynthesis of the leinamycin (LNM) family of natural products, exemplified by LnmJ-SH and guangnanmycin (GnmT-SH). Here we report a detailed investigation into the PLP-dependent reaction catalyzed by the SH domains, guided by a 1.8 Å resolution crystal structure of GnmT-SH. A series of elaborate substrate mimics were synthesized to answer specific questions garnered from the crystal structure and from the biosynthetic logic of the LNM family of natural products. Through a combination of bioinformatics, molecular modeling, in vitro assays, and mutagenesis, we have developed a detailed model of acyl carrier protein (ACP)-tethered substrate-SH, and interdomain interactions, that contribute to the observed substrate specificity. Comparison of the GnmT-SH structure with archetypical PLP-dependent enzyme structures revealed how Nature, via evolution, has modified a common protein structural motif to accommodate an ACP-tethered substrate, which is significantly larger than any of those previously characterized. Overall, this study demonstrates how PLP-dependent chemistry can be incorporated into the context of PKS assembly lines and sets the stage for engineering PKSs to produce sulfur-containing polyketides.

PubMed: 39546807
DOI: 10.1021/jacs.4c11656

Experimental method

X-RAY DIFFRACTION (1.8 Å)