The third adenylation domain of the fungal SidN non-ribosomal peptide synthetase

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis

Lee, T.V.Johnson, L.J.Johnson, R.D.Koulman, A.Lane, G.A.Lott, J.S.Arcus, V.L.

(2010) J Biol Chem 285: 2415-2427

  • DOI: https://doi.org/10.1074/jbc.M109.071324
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Nonribosomal peptide synthetases (NRPSs) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. We report the structure of the third adenylation domain from the siderophore-synthesizing NRPS, SidN, from the endophytic fungus Neotyphodium lolii. This is the first structure of a eukaryotic NRPS domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, N(delta)-cis-anhydromevalonyl-N(delta)-hydroxy-L-ornithine (cis-AMHO). The specific activation of cis-AMHO was confirmed biochemically, and an AMHO moiety was unambiguously identified as a component of the fungal siderophore using mass spectroscopy. The protein structure shows that the substrate binding pocket is defined by 17 amino acid residues, in contrast to both prokaryotic adenylation domains and to previous predictions based on modeling. Existing substrate prediction methods for NRPS adenylation domains fail for domains from eukaryotes due to the divergence of their signature sequences from those of prokaryotes. Thus, this new structure will provide a basis for improving prediction methods for eukaryotic NRPS enzymes that play important and diverse roles in the biology of fungi.

  • Organizational Affiliation

    AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SidN siderophore synthetase
A, B
562Epichloe festucae var. loliiMutation(s): 0 
Gene Names: sidN
Find proteins for K7NCP5 (Epichloe festucae var. lolii)
Explore K7NCP5 
Go to UniProtKB:  K7NCP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7NCP5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.598α = 114.85
b = 75.28β = 94.78
c = 84.137γ = 90.18
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Database references