1W3V

Isopenicillin N synthase d-(L-a-aminoadipoyl)-(3R)-methyl-L-cysteine D-a-hydroxyisovaleryl ester complex (anaerobic)

Summary for 1W3V

• Entry DOI: 10.2210/pdb1w3v/pdb
• Related: 1BK0 1BLZ 1HB1 1HB2 1HB3 1HB4 1IPS 1OBN 1OC1 1ODM 1ODN 1QIQ 1QJE 1QJF 1UZW 1W03 1W04 1W05 1W06 1W3X 2BJS 2BU9
• Descriptor: ISOPENICILLIN N SYNTHETASE, FE (II) ION, N~6~-METHYL-6-OXO-L-LYSINE - 2-[(3-MERCAPTOBUTANOYL)OXY]-3-METHYLBUTANOIC ACID, ... (4 entities in total)
• Functional Keywords: synthase, antibiotic biosynthesis, b-lactam antibiotic, iron, oxidoreductase, oxygenase, penicillin biosynthesis
• Biological source: Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans)
• Total number of polymer chains: 1
• Total formula weight: 37998.12

Authors

Daruzzaman, A.,Clifton, I.J.,Rutledge, P.J. (deposition date: 2004-07-20, release date: 2005-12-07, Last modification date: 2024-05-08)

Primary citation

Daruzzaman, A.,Clifton, I.J.,Adlington, R.M.,Baldwin, J.E.,Rutledge, P.J.
Unexpected Oxidation of a Depsipeptide Substrate Analogue in Crystalline Isopenicillin N Synthase.
Chembiochem, 7:351-, 2006

PubMed Abstract: Isopenicillin N synthase (IPNS) is a non-heme iron(ii)-dependent oxidase that is central to penicillin biosynthesis. Herein, we report mechanistic studies of the IPNS reaction in the crystalline state, using the substrate analogue delta-(L-alpha-aminoadipoyl)-(3R)-methyl-L-cysteine D-alpha-hydroxyisovaleryl ester (AmCOV) to probe the early stages of the catalytic cycle. The X-ray crystal structure of the anaerobic IPNS:Fe(II):AmCOV complex was solved to 1.40 A resolution, and it reveals several subtle differences in the active site relative to the complex of the enzyme with its natural substrate. The crystalline IPNS:Fe(II):AmCOV complex was then exposed to oxygen gas at high pressure; this brought about reaction to give what appears to be a hydroxymethyl/ene-thiol product. A mechanism for this reaction is proposed. These results offer further insight into the delicate interplay of steric and electronic effects in the IPNS active site and the mechanistic intricacies of this remarkable enzyme.

PubMed: 16444759
DOI: 10.1002/CBIC.200500282

Experimental method

X-RAY DIFFRACTION (1.4 Å)