7THN

Crystal structure of PigI trapped with PigG using a proline adenosine vinylsulfonamide inhibitor

Summary for 7THN

• Entry DOI: 10.2210/pdb7thn/pdb
• Descriptor: L-proline--[L-prolyl-carrier protein] ligase, Probable acyl carrier protein PigG, GLYCEROL, ... (7 entities in total)
• Functional Keywords: nonribosomal peptide synthetase, nrps, type ii, biosynthesis, ligase-transport protein complex, ligase
• Biological source: Serratia sp. ATCC 39006; More
• Total number of polymer chains: 2
• Total formula weight: 67067.38

Authors

Corpuz, J.C.,Podust, L.M. (deposition date: 2022-01-11, release date: 2022-11-30, Last modification date: 2024-11-06)

Primary citation

Corpuz, J.C.,Patel, A.,Davis, T.D.,Podust, L.M.,McCammon, J.A.,Burkart, M.D.
Essential Role of Loop Dynamics in Type II NRPS Biomolecular Recognition.
Acs Chem.Biol., 17:2890-2898, 2022

PubMed Abstract: Non-ribosomal peptides play a critical role in the clinic as therapeutic agents. To access more chemically diverse therapeutics, non-ribosomal peptide synthetases (NRPSs) have been targeted for engineering through combinatorial biosynthesis; however, this has been met with limited success in part due to the lack of proper protein-protein interactions between non-cognate proteins. Herein, we report our use of chemical biology to enable X-ray crystallography, molecular dynamics (MD) simulations, and biochemical studies to elucidate binding specificities between peptidyl carrier proteins (PCPs) and adenylation (A) domains. Specifically, we determined X-ray crystal structures of a type II PCP crosslinked to its cognate A domain, PigG and PigI, and of PigG crosslinked to a non-cognate PigI homologue, PltF. The crosslinked PCP-A domain structures possess large protein-protein interfaces that predominantly feature hydrophobic interactions, with specific electrostatic interactions that orient the substrate for active site delivery. MD simulations of the PCP-A domain complexes and unbound PCP structures provide a dynamical evaluation of the transient interactions formed at PCP-A domain interfaces, which confirm the previously hypothesized role of a PCP loop as a crucial recognition element. Finally, we demonstrate that the interfacial interactions at the PCP loop 1 region can be modified to control PCP binding specificity through gain-of-function mutations. This work suggests that loop conformational preferences and dynamism account for improved shape complementary in the PCP-A domain interactions. Ultimately, these studies show how crystallographic, biochemical, and computational methods can be used to rationally re-engineer NRPSs for non-cognate interactions.

PubMed: 36173802
DOI: 10.1021/acschembio.2c00523

Experimental method

X-RAY DIFFRACTION (1.6 Å)