1BK0

ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV-FE COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.172 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation.

Roach, P.L.Clifton, I.J.Hensgens, C.M.Shibata, N.Schofield, C.J.Hajdu, J.Baldwin, J.E.

(1997) Nature 387: 827-830

  • DOI: https://doi.org/10.1038/42990
  • Primary Citation of Related Structures:  
    1BK0, 1BLZ

  • PubMed Abstract: 

    The biosynthesis of penicillin and cephalosporin antibiotics in microorganisms requires the formation of the bicyclic nucleus of penicillin. Isopenicillin N synthase (IPNS), a non-haem iron-dependent oxidase, catalyses the reaction of a tripeptide, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV), and dioxygen to form isopenicillin N and two water molecules. Mechanistic studies suggest the reaction is initiated by ligation of the substrate thiolate to the iron centre, and proceeds through an enzyme-bound monocyclic intermediate. Here we report the crystal structure of IPNS complexed to ferrous iron and ACV, determined to 1.3 A resolution. Based on the structure, we propose a mechanism for penicillin formation that involves ligation of ACV to the iron centre, creating a vacant iron coordination site into which dioxygen can bind. Subsequently, iron-dioxygen and iron-oxo species remove the requisite hydrogens from ACV without the direct assistance of protein residues. The crystal structure of the complex with the dioxygen analogue, NO and ACV bound to the active-site iron supports this hypothesis.


  • Organizational Affiliation

    The Dyson Perrins Laboratory, University of Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ISOPENICILLIN N SYNTHASE331Aspergillus nidulansMutation(s): 0 
Gene Names: PCB C
EC: 1.21.3.1
UniProt
Find proteins for P05326 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore P05326 
Go to UniProtKB:  P05326
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05326
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.8α = 90
b = 71.5β = 90
c = 101γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection