1QJF

ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (Monocyclic Sulfoxide - Fe COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Observed: 0.131 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history


Literature

The Reaction Cycle of Isopenicillin N Synthase Observed by X-Ray Diffraction

Burzlaff, N.I.Rutledge, P.J.Clifton, I.J.Hensgens, C.M.H.Pickford, M.Adlington, R.M.Roach, P.L.Baldwin, J.E.

(1999) Nature 401: 721

  • DOI: https://doi.org/10.1038/44400
  • Primary Citation of Related Structures:  
    1QIQ, 1QJE, 1QJF

  • PubMed Abstract: 

    Isopenicillin N synthase (IPNS), a non-haem iron-dependent oxidase, catalyses the biosynthesis of isopenicillin N (IPN), the precursor of all penicillins and cephalosporins. The key steps in this reaction are the two iron-dioxygen-mediated ring closures of the tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV). It has been proposed that the four-membered beta-lactam ring forms initially, associated with a highly oxidized iron(iv)-oxo (ferryl) moiety, which subsequently mediates closure of the five-membered thiazolidine ring. Here we describe observation of the IPNS reaction in crystals by X-ray crystallography. IPNS Fe2+ substrate crystals were grown anaerobically, exposed to high pressures of oxygen to promote reaction and frozen, and their structures were elucidated by X-ray diffraction. Using the natural substrate ACV, this resulted in the IPNS x Fe2+ x IPN product complex. With the substrate analogue, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-L-S-methylcysteine (ACmC) in the crystal, the reaction cycle was interrupted at the monocyclic stage. These mono- and bicyclic structures support our hypothesis of a two-stage reaction sequence leading to penicillin. Furthermore, the formation of a monocyclic sulphoxide product from ACmC is most simply explained by the interception of a high-valency iron-oxo species.


  • Organizational Affiliation

    The Dyson Perrins Laboratory and the Oxford Centre for Molecular Sciences, University of Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ISOPENICILLIN N SYNTHASE331Aspergillus nidulans FGSC A4Mutation(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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACS
Query on ACS

Download Ideal Coordinates CCD File 
C [auth A]1-[(1S)-CARBOXY-2-(METHYLSULFINYL)ETHYL]-(3R)-[(5S)-5-AMINO-5-CARBOXYPENTANAMIDO]-(4R)-SULFANYLAZETIDIN-2-ONE
C13 H21 N3 O7 S2
UFLVUEXXBDLOEJ-QUNHDKFLSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE2
Query on FE2

Download Ideal Coordinates CCD File 
D [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Observed: 0.131 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.777α = 90
b = 71.186β = 90
c = 101.251γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXLphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-10-24
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2019-07-10
    Changes: Data collection
  • Version 1.5: 2019-07-24
    Changes: Data collection
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.7: 2024-05-08
    Changes: Source and taxonomy