8K4R

Structure of VinM-VinL complex

Summary for 8K4R

• Entry DOI: 10.2210/pdb8k4r/pdb
• Descriptor: Non-ribosomal peptide synthetase, Acyl-carrier-protein, SODIUM ION, ... (5 entities in total)
• Functional Keywords: complex, adenylation enzyme, atp, carrier protein, biosynthesis, ligase
• Biological source: Streptomyces halstedii; More
• Total number of polymer chains: 4
• Total formula weight: 140623.97

Authors

Miyanaga, A.,Nagata, K.,Nakajima, J.,Chisuga, T.,Kudo, F.,Eguchi, T. (deposition date: 2023-07-20, release date: 2023-11-01, Last modification date: 2024-10-16)

Primary citation

Miyanaga, A.,Nagata, K.,Nakajima, J.,Chisuga, T.,Kudo, F.,Eguchi, T.
Structural Basis of Amide-Forming Adenylation Enzyme VinM in Vicenistatin Biosynthesis.
Acs Chem.Biol., 18:2343-2348, 2023

PubMed Abstract: Adenylation enzymes activate amino acid substrates to aminoacyl adenylates and generally transfer this moiety onto the thiol group of the phosphopantetheine arm of a carrier protein for the selective incorporation of aminoacyl building blocks in natural product biosynthesis. In contrast to the canonical thioester-forming adenylation enzymes, the amide-forming adenylation enzyme VinM transfers an l-alanyl group onto the amino group of the aminoacyl unit attached to the phosphopantetheine arm of the carrier protein VinL to generate dipeptidyl-VinL in vicenistatin biosynthesis. It is unclear how VinM distinguishes aminoacyl-VinL from VinL for amide bond formation. Herein we describe structural and biochemical analyses of VinM. We determined the crystal structure of VinM in complex with VinL using a designed pantetheine-type cross-linking probe. The VinM-VinL complex structure in combination with site-directed mutagenesis analysis revealed that the interactions with both the phosphopantetheine arm and VinL are critical for the amide-forming activity of VinM.

PubMed: 37870408
DOI: 10.1021/acschembio.3c00517

Experimental method

X-RAY DIFFRACTION (2.3 Å)