Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.17 kDa 
• Atom Count: 3001 
• Modelled Residue Count: 329 
• Deposited Residue Count: 331 
• Unique protein chains: 1

1W04

Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Glycine-Fe-NO Complex

• PDB DOI: 10.2210/pdb1W04/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus nidulans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-06-01 Released: 2005-05-04 
• Deposition Author(s): Long, A.J., Clifton, I.J., Rutledge, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.175 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Structural Studies on the Reaction of Isopenicillin N Synthase with the Truncated Substrate Analogues Delta-(L-Alpha-Aminoadipoyl)-L-Cysteinyl-Glycine and Delta-(L-Alpha-Aminoadipoyl)-L-Cysteinyl-D- Alanine

Long, A.J., Clifton, I.J., Roach, P.L., Baldwin, J.E., Schofield, C.J., Rutledge, P.J.

(2005) Biochemistry 44: 6619

• PubMed: 15850395 
• DOI: 10.1021/bi047478q
• Primary Citation of Related Structures:  
  1W03, 1W04, 1W05, 1W06


• PubMed Abstract: 
  

Isopenicillin N synthase (IPNS), a non-heme iron(II)-dependent oxidase, catalyzes conversion of the tripeptide delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-valine (ACV) to bicyclic isopenicillin N (IPN), concomitant with the reduction of dioxygen to two molecules of water. Incubation of the "truncated"substrate analogues delta-(l-alpha-aminoadipoyl)-l-cysteinyl-glycine (ACG) and delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-alanine (ACA) with IPNS has previously been shown to afford acyclic products, in which the substrate cysteinyl residue has undergone a two-electron oxidation. We report X-ray crystal structures for the anaerobic IPNS/Fe(II)/ACG and IPNS/Fe(II)/ACA complexes, both in the absence and presence of the dioxygen analogue nitric oxide. The overall protein structures are very similar to those of the corresponding IPNS/Fe(II)/ACV complexes; however, significant differences are apparent in the vicinity of the active site iron. The structure of the IPNS/Fe(II)/ACG complex reveals that the C-terminal carboxylate of this substrate is oriented toward the active site iron atom, apparently hydrogen-bonded to an additional water ligand at the metal; this is a different binding mode to that observed in the IPNS/Fe(II)/ACV complex. ACA binds to the metal in a manner that is intermediate between those observed for ACV and ACG. The addition of NO to these complexes initiates conformational changes such that both the IPNS/Fe(II)/ACG/NO and IPNS/Fe(II)/ACA/NO structures closely resemble the IPNS/Fe(II)/ACV/NO complex. These results further demonstrate the feasibility of metal-centered rearrangements in catalysis by non-heme iron enzymes and provide insight into the delicate balance between hydrophilic-hydrophobic interactions and steric effects in the IPNS active site.

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Organizational Affiliation: 

Chemistry Research Laboratory, University of Oxford, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ISOPENICILLIN N SYNTHETASE	A	331	Aspergillus nidulans	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCG	B [auth A]	DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-GLYCINE C11 H19 N3 O6 S XFOOPZIJVVDYHI-BQBZGAKWSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE2	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
HOA	D [auth A]	HYDROXYAMINE H3 N O AVXURJPOCDRRFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.175 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.652	α = 90
b = 70.752	β = 90
c = 100.973	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-06-01 
• Released Date: 2005-05-04 
Deposition Author(s): Long, A.J., Clifton, I.J., Rutledge, P.J.

Revision History  

• Version 1.0: 2005-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance