1QIQ

ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACmC Fe COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 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) ...

    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.


    Related Citations: 
    • 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
    • Crystal Structure of Isopenicillin N Synthase is the First from a New Structural Family of Enzymes
      Roach, P.L., Clifton, I.J., Fulop, V., Harlos, K., Barton, G.J., Hajdu, J., Andersson, I., Schofield, C.J., Baldwin, J.E.
      (1995) Nature 375: 700
    • Crystallization and Preliminary X-Ray Diffraction Studies on Recombinant Isopenicillin N Synthase from Aspergillus Nidulans
      Roach, P.L., Schofield, C.J., Baldwin, J.E., Clifton, I.J., Hajdu, J.
      (1995) Protein Sci 4: 1007

    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
MoleculeChainsSequence LengthOrganismDetailsImage
ISOPENICILLIN N SYNTHASEA331Aspergillus 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACC
Query on ACC

Download Ideal Coordinates CCD File 
B [auth A]N-[N-[2-AMINO-6-OXO-HEXANOIC ACID-6-YL]CYSTEINYL]-S-METHYLCYSTEINE
C13 H24 N3 O6 S2
FTCBRKCNMSXWJP-XHNCKOQMSA-O
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.81α = 90
b = 71.66β = 90
c = 101.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-16
    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: 2017-07-05
    Changes: Refinement description
  • Version 1.4: 2018-10-24
    Changes: Data collection, Source and taxonomy