5ES8

Crystal structure of the initiation module of LgrA in the thiolation state

Summary for 5ES8

• Entry DOI: 10.2210/pdb5es8/pdb
• Related: 5ES5 5ES6 5ES7 5ES9
• Descriptor: Linear gramicidin synthetase subunit A, [(3~{R})-4-[[3-[2-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate (3 entities in total)
• Functional Keywords: nrps, formylation domain, adenylation domain, peptidyl carrier protein, ligase
• Biological source: Brevibacillus parabrevis
• Total number of polymer chains: 2
• Total formula weight: 177007.22

Authors

Reimer, J.M.,Aloise, M.N.,Schmeing, T.M. (deposition date: 2015-11-16, release date: 2016-01-20, Last modification date: 2024-11-13)

Primary citation

Reimer, J.M.,Aloise, M.N.,Harrison, P.M.,Schmeing, T.M.
Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase.
Nature, 529:239-242, 2016

PubMed Abstract: Nonribosomal peptide synthetases (NRPSs) are very large proteins that produce small peptide molecules with wide-ranging biological activities, including environmentally friendly chemicals and many widely used therapeutics. NRPSs are macromolecular machines, with modular assembly-line logic, a complex catalytic cycle, moving parts and many active sites. In addition to the core domains required to link the substrates, they often include specialized tailoring domains, which introduce chemical modifications and allow the product to access a large expanse of chemical space. It is still unknown how the NRPS tailoring domains are structurally accommodated into megaenzymes or how they have adapted to function in nonribosomal peptide synthesis. Here we present a series of crystal structures of the initiation module of an antibiotic-producing NRPS, linear gramicidin synthetase. This module includes the specialized tailoring formylation domain, and states are captured that represent every major step of the assembly-line synthesis in the initiation module. The transitions between conformations are large in scale, with both the peptidyl carrier protein domain and the adenylation subdomain undergoing huge movements to transport substrate between distal active sites. The structures highlight the great versatility of NRPSs, as small domains repurpose and recycle their limited interfaces to interact with their various binding partners. Understanding tailoring domains is important if NRPSs are to be utilized in the production of novel therapeutics.

PubMed: 26762462
DOI: 10.1038/nature16503

Experimental method

X-RAY DIFFRACTION (2.547 Å)