5IG8

Crystal structure of macrocyclase MdnB from Microcystis aeruginosa MRC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.278 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for precursor protein-directed ribosomal peptide macrocyclization.

Li, K.Condurso, H.L.Li, G.Ding, Y.Bruner, S.D.

(2016) Nat.Chem.Biol. 12: 973-979

  • DOI: 10.1038/nchembio.2200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, University of Florida, Gainesville, Florida, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP grasp ligase
A, B
335Microcystis aeruginosa MRCMutation(s): 0 
Gene Names: mdnB
Find proteins for B2G3C9 (Microcystis aeruginosa MRC)
Go to UniProtKB:  B2G3C9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.278 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.623α = 90.00
b = 37.990β = 116.55
c = 139.385γ = 90.00
Software Package:
Software NamePurpose
BUCCANEERmodel building
XDSdata reduction
Aimlessdata scaling
ARP/wARPmodel building
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references
  • Version 1.2: 2016-10-26
    Type: Database references