5IG9 image
Deposition Date 2016-02-27
Release Date 2016-09-21
Last Version Date 2024-03-06
Entry Detail
PDB ID:
5IG9
Keywords:
Title:
Crystal structure of macrocyclase MdnC bound with precursor peptide MdnA from Microcystis aeruginosa MRC
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.67 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 41
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ATP grasp ligase
Gene (Uniprot):mdnC
Chain IDs:A, B, C, D, E, F, G, H
Chain Length:333
Number of Molecules:8
Biological Source:Microcystis aeruginosa MRC
Polymer Type:polypeptide(L)
Molecule:Microviridin
Gene (Uniprot):mdnA
Chain IDs:I (auth: P), J (auth: I), K (auth: J), L (auth: K), M (auth: L), N (auth: M), O (auth: N), P (auth: O)
Chain Length:49
Number of Molecules:8
Biological Source:Microcystis aeruginosa MRC
Ligand Molecules
Primary Citation
Structural basis for precursor protein-directed ribosomal peptide macrocyclization.
Nat.Chem.Biol. 12 973 979 (2016)
PMID: 27669417 DOI: 10.1038/nchembio.2200

Abstact

Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides that target proteases with potent reversible inhibition. The product structure is constructed via three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here we describe in detail the structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases MdnC and MdnB interact with a conserved α-helix of the precursor peptide using a novel precursor-peptide recognition mechanism. The results provide insight into the unique protein-protein interactions that are key to the chemistry, suggest an origin for the natural combinatorial synthesis of microviridin peptides, and provide a framework for future engineering efforts to generate designed compounds.

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Primary Citation of related structures