2BU9 | pdb_00002bu9

Isopenicillin N synthase complexed with L-aminoadipoyl-L-cysteinyl-L- hexafluorovaline

• PDB DOI: https://doi.org/10.2210/pdb2BU9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus nidulans FGSC A4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-09 Released: 2005-09-15 
• Deposition Author(s): Howard-Jones, A.R., Rutledge, P.J., Clifton, I.J., Adlington, R.M., Baldwin, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Unique Binding of a Non-Natural L,L,L-Substrate by Isopenicillin N Synthase

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

(2005) Biochem Biophys Res Commun 336: 702

• PubMed: 16143309 
• DOI: https://doi.org/10.1016/j.bbrc.2005.08.155
• Primary Citation of Related Structures:  
  2BU9


• PubMed Abstract: 
  

  Isopenicillin N synthase (IPNS) is a non-haem iron oxidase that catalyses the formation of isopenicillin N from the tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine. In this report, we describe the crystal structure of the enzyme with a non-natural L,L,L-tripeptide substrate, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-L-3,3,3,3',3',3'-hexafluorovaline. This structure reveals a strong binding interaction of the tripeptide within the active site and a unique conformation for the non-natural L,L,L-diastereomer. Taken together, these findings provide a possible rationale for the previously observed inhibitory effects of L,L,L-tripeptide substrates on IPNS activity.

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Organizational Affiliation: 
• Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 38.19 kDa 
• Atom Count: 3,170 
• Modeled Residue Count: 329 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ISOPENICILLIN N SYNTHETASE	A	331	Aspergillus nidulans FGSC A4	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HFV	C [auth A]	DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-L-3,3,3,3',3',3'-HEXAFLUOROVALINE C14 H19 F6 N3 O6 S IPFVQRRDLLEXCD-HAFWLYHUSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.465	α = 90
b = 71.012	β = 90
c = 100.768	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-15 
Deposition Author(s): Howard-Jones, A.R., Rutledge, P.J., Clifton, I.J., Adlington, R.M., Baldwin, J.E.

Revision History  

• Version 1.0: 2005-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-05-08
  Changes: Source and taxonomy