5IG9 | pdb_00005ig9

Crystal structure of macrocyclase MdnC bound with precursor peptide MdnA from Microcystis aeruginosa MRC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.261 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.219 (Depositor) 
  • R-Value Observed: 
    0.229 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5IG9

This is version 1.3 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: https://doi.org/10.1038/nchembio.2200
  • Primary Citation Related Structures: 
    5IG8, 5IG9

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 349.62 kDa 
  • Atom Count: 20,643 
  • Modeled Residue Count: 2,575 
  • Deposited Residue Count: 3,056 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP grasp ligase
A, B, C, D, E
A, B, C, D, E, F, G, H
333Microcystis aeruginosa MRCMutation(s): 0 
Gene Names: mdnC
UniProt
Find proteins for B2G3D0 (Microcystis aeruginosa MRC)
Explore B2G3D0 
Go to UniProtKB:  B2G3D0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2G3D0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Microviridin49Microcystis aeruginosa MRCMutation(s): 0 
UniProt
Find proteins for B2G3C8 (Microcystis aeruginosa MRC)
Explore B2G3C8 
Go to UniProtKB:  B2G3C8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2G3C8
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.261 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.219 (Depositor) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.56α = 90
b = 132.56β = 90
c = 198.157γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-12
    Changes: Database references
  • Version 1.2: 2016-10-26
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations