1UZW

ISOPENICILLIN N SYNTHASE WITH L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-ISODEHYDROVALINE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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This is version 1.2 of the entry. See complete history. 


Literature

Active Site Mediated Elimination of Hydrogen Fluoride from a Fluorinated Substrate Analogue by Isopenicillin N Synthase

Grummitt, A.R., Rutledge, P.J., Clifton, I.J., Baldwin, J.E.

(2004) Biochem J 382: 659

  • DOI: 10.1042/BJ20040529
  • Primary Citation of Related Structures:  
    1UZW

  • PubMed Abstract: 

    • Isopenicillin N synthase (IPNS) is a non-haem iron oxidase that catalyses the formation of bicyclic isopenicillin N from delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV). In this study we report a novel activity for the iron of the IPNS active site, which behaves as a Lewis acid to catalyse the elimination of HF from the fluorinated substrate analogue, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-beta-fluorovaline (ACbetaFV) ...

    Isopenicillin N synthase (IPNS) is a non-haem iron oxidase that catalyses the formation of bicyclic isopenicillin N from delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV). In this study we report a novel activity for the iron of the IPNS active site, which behaves as a Lewis acid to catalyse the elimination of HF from the fluorinated substrate analogue, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-beta-fluorovaline (ACbetaFV). X-Ray crystallographic studies of IPNS crystals grown anaerobically with ACbetaFV reveal that the valinyl beta-fluorine is missing from the active site region, and suggest the presence of the unsaturated tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-isodehydrovaline in place of substrate ACbetaFV. (19)F NMR studies confirm the release of fluoride from ACbetaFV in the presence of the active IPNS enzyme. These results suggest a new mode of reactivity for the IPNS iron centre, a mechanism of action that has not previously been reported for any of the iron oxidase enzymes.

    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
    • 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: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ISOPENICILLIN N SYNTHETASEA331Aspergillus nidulansMutation(s): 0 
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDH
Query on CDH
Download Ideal Coordinates CCD File 
C [auth A]D-(L-A-AMINOADIPOYL)-L-CYSTEINYL-D-ISODEHYDROVALINE
C14 H23 N3 O6 S
BGZJEMYSINIAHS-NWGYLPEXSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.228α = 90
b = 70.595β = 90
c = 100.639γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-10
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance