1QIQ

ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACmC Fe COMPLEX)

PDB DOI: 10.2210/pdb1QIQ/pdb

Classification: ANTIBIOTIC BIOSYNTHESIS
Organism(s): Aspergillus nidulans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-06-15 Released: 2000-06-16
Deposition Author(s): Rutledge, P.J., Clifton, I.J., Burzlaff, N.I., Roach, P.L., Adlington, R.M., Baldwin, J.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.199
R-Value Work: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The Reaction Cycle of Isopenicillin N Synthase Observed by X-Ray Diffraction.

Burzlaff, N.I., Rutledge, P.J., Clifton, I.J., Hensgens, C.M.H., Pickford, M., Adlington, R.M., Roach, P.L., Baldwin, J.E.

(1999) Nature 401: 721

PubMed: 10537113 Search on PubMed
DOI: 10.1038/44400
Primary Citation of Related Structures:
1QIQ, 1QJE, 1QJF

PubMed Abstract:

Isopenicillin N synthase (IPNS), a non-haem iron-dependent oxidase, catalyses the biosynthesis of isopenicillin N (IPN), the precursor of all penicillins and cephalosporins. The key steps in this reaction are the two iron-dioxygen-mediated ring closures of the tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV). It has been proposed that the four-membered beta-lactam ring forms initially, associated with a highly oxidized iron(iv)-oxo (ferryl) moiety, which subsequently mediates closure of the five-membered thiazolidine ring. Here we describe observation of the IPNS reaction in crystals by X-ray crystallography. IPNS Fe2+ substrate crystals were grown anaerobically, exposed to high pressures of oxygen to promote reaction and frozen, and their structures were elucidated by X-ray diffraction. Using the natural substrate ACV, this resulted in the IPNS x Fe2+ x IPN product complex. With the substrate analogue, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-L-S-methylcysteine (ACmC) in the crystal, the reaction cycle was interrupted at the monocyclic stage. These mono- and bicyclic structures support our hypothesis of a two-stage reaction sequence leading to penicillin. Furthermore, the formation of a monocyclic sulphoxide product from ACmC is most simply explained by the interception of a high-valency iron-oxo species.

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

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

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:

The Dyson Perrins Laboratory and the Oxford Centre for Molecular Sciences, University of Oxford, UK.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ISOPENICILLIN N SYNTHASE	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05326
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACC Query on ACC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-[N-[2-AMINO-6-OXO-HEXANOIC ACID-6-YL]CYSTEINYL]-S-METHYLCYSTEINE C₁₃ H₂₄ N₃ O₆ S₂ FTCBRKCNMSXWJP-XHNCKOQMSA-O		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Ligand Interaction