1BK0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/42990
  • Primary Citation of Related Structures:  1BLZ
  • Also Cited By: 1HB1, 1HB2, 1HB3, 1HB4, 1OBN, 1OC1, 1ODM, 1ODN, 1QIQ, 1QJE, 1QJF, 1UZW, 2IVI, 2IVJ

  • 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, d ...

    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.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    The Dyson Perrins Laboratory, University of Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ISOPENICILLIN N SYNTHASE
A
331Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)Gene Names: ipnA (ips)
EC: 1.21.3.1
Find proteins for P05326 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Go to UniProtKB:  P05326
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACV
Query on ACV

Download SDF File 
Download CCD File 
A
L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE
C14 H25 N3 O6 S
BYEIJZFKOAXBBV-ATZCPNFKSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.800α = 90.00
b = 71.500β = 90.00
c = 101.000γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance