5U89

Crystal structure of a cross-module fragment from the dimodular NRPS DhbF

Summary for 5U89

• Entry DOI: 10.2210/pdb5u89/pdb
• Descriptor: Amino acid adenylation domain protein, MbtH domain protein, 5'-({[(2R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}propyl]sulfonyl}amino)-5'-deoxyadenosine (3 entities in total)
• Functional Keywords: nonribosomal peptide synthetase, mbth-like protein, mechanism-based inhibitor, megaenzyme, hydrolase-inhibitor complex, hydrolase/inhibitor
• Biological source: Geobacillus sp.; More
• Total number of polymer chains: 2
• Total formula weight: 131335.11

Authors

Tarry, M.J.,Schmeing, T.M. (deposition date: 2016-12-14, release date: 2017-05-10, Last modification date: 2024-10-23)

Primary citation

Tarry, M.J.,Haque, A.S.,Bui, K.H.,Schmeing, T.M.
X-Ray Crystallography and Electron Microscopy of Cross- and Multi-Module Nonribosomal Peptide Synthetase Proteins Reveal a Flexible Architecture.
Structure, 25:783-793.e4, 2017

PubMed Abstract: Nonribosomal peptide synthetases (NRPS) are macromolecular machines that produce peptides with diverse activities. Structural information exists for domains, didomains, and even modules, but little is known about higher-order organization. We performed a multi-technique study on constructs from the dimodular NRPS DhbF. We determined a crystal structure of a cross-module construct including the adenylation (A) and peptidyl carrier protein (PCP) domains from module 1 and the condensation domain from module 2, complexed with an adenosine-vinylsulfonamide inhibitor and an MbtH-like protein (MLP). The action of the inhibitor and the role of the MLP were investigated using adenylation reactions and isothermal titration calorimetry. In the structure, the PCP and A domains adopt a novel conformation, and noncovalent, cross-module interactions are limited. We calculated envelopes of dimodular DhbF using negative-stain electron microscopy. The data show large conformational variability between modules. Together, our results suggest that NRPSs lack a uniform, rigid supermodular architecture.

PubMed: 28434915
DOI: 10.1016/j.str.2017.03.014

Experimental method

X-RAY DIFFRACTION (3.075 Å)