2IVJ

Isopenicillin N Synthase From Aspergillus Nidulans (Anaerobic Ac- cyclopropylglycine Fe Complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Interactions of Isopenicillin N Synthase with Cyclopropyl-Containing Substrate Analogues Reveal New Mechanistic Insight.

Howard-Jones, A.R.Elkins, J.M.Clifton, I.J.Roach, P.L.Adlington, R.M.Baldwin, J.E.Rutledge, P.J.

(2007) Biochemistry 46: 4755

  • DOI: 10.1021/bi062314q
  • Primary Citation of Related Structures:  
    2IVJ, 2IVI

  • PubMed Abstract: 
  • Isopenicillin N synthase (IPNS), a non-heme iron oxidase central to penicillin and cephalosporin biosynthesis, catalyzes an energetically demanding chemical transformation to produce isopenicillin N from the tripeptide delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-valine (ACV) ...

    Isopenicillin N synthase (IPNS), a non-heme iron oxidase central to penicillin and cephalosporin biosynthesis, catalyzes an energetically demanding chemical transformation to produce isopenicillin N from the tripeptide delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-valine (ACV). We describe the synthesis of two cyclopropyl-containing tripeptide analogues, delta-(l-alpha-aminoadipoyl)-l-cysteinyl-beta-methyl-d-cyclopropylglycine and delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-cyclopropylglycine, designed as probes for the mechanism of IPNS. We have solved the X-ray crystal structures of these substrates in complex with IPNS and propose a revised mechanism for the IPNS-mediated turnover of these compounds. Relative to the previously determined IPNS-Fe(II)-ACV structure, key differences exist in substrate orientation and water occupancy, which allow for an explanation of the differences in reactivity of these substrates.


    Related Citations: 
    • The Reaction Cycle of Isopenicillin N Synthase Observed by X-Ray Diffraction
      Burzlaff, N.I., Rutledge, P.J., Clifton, I.J., Hensgens, C.M., Pickford, M., Adlington, R.M., Roach, P.L., Baldwin, J.E.
      (1999) Nature 401: 721
    • 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: 300

    Organizational Affiliation

    Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ISOPENICILLIN N SYNTHETASEA331Aspergillus nidulansMutation(s): 0 
EC: 1.21.3.1
Find proteins for P05326 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore P05326 
Go to UniProtKB:  P05326
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCV
Query on BCV

Download Ideal Coordinates CCD File 
B [auth A]D-(L-A-AMINOADIPOYL)-L-CYSTEINYL-D-CYCLOPROPYLGLYCINE
C14 H23 N3 O6 S
QDTDEZBVMFHOLY-ATZCPNFKSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE2
Query on FE2

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.663α = 90
b = 71.182β = 90
c = 100.877γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references, Derived calculations, Other, Version format compliance