1HB4

ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.182 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

Alternative Oxidation by Isopenicillin N Synthase Observed by X-Ray Diffraction.

Ogle, J.M.Clifton, I.J.Rutledge, P.J.Elkins, J.M.Burzlaff, N.I.M Adlington, R.Roach, P.L.Baldwin, J.E.

(2001) Chem Biol 8: 1231

  • DOI: https://doi.org/10.1016/s1074-5521(01)00090-4
  • Primary Citation of Related Structures:  
    1HB1, 1HB2, 1HB3, 1HB4

  • PubMed Abstract: 

    Isopenicillin N synthase (IPNS) catalyses formation of bicyclic isopenicillin N, precursor to all penicillin and cephalosporin antibiotics, from the linear tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine. IPNS is a non-haem iron(II)-dependent enzyme which utilises the full oxidising potential of molecular oxygen in catalysing the bicyclisation reaction. The reaction mechanism is believed to involve initial formation of the beta-lactam ring (via a thioaldehyde intermediate) to give an iron(IV)-oxo species, which then mediates closure of the 5-membered thiazolidine ring. Here we report experiments employing time-resolved crystallography to observe turnover of an isosteric substrate analogue designed to intercept the catalytic pathway at an early stage. Reaction in the crystalline enzyme-substrate complex was initiated by the application of high-pressure oxygen, and subsequent flash freezing allowed an oxygenated product to be trapped, bound at the iron centre. A mechanism for formation of the observed thiocarboxylate product is proposed. In the absence of its natural reaction partner (the N-H proton of the L-cysteinyl-D-valine amide bond), the proposed hydroperoxide intermediate appears to attack the putative thioaldehyde species directly. These results shed light on the events preceding beta-lactam closure in the IPNS reaction cycle, and enhance our understanding of the mechanism for reaction of the enzyme with its natural substrate.


  • 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 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.66α = 90
b = 71.21β = 90
c = 100.17γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata 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: 2001-11-23
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Refinement description
  • Version 1.4: 2018-10-24
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.6: 2024-05-08
    Changes: Source and taxonomy