2VBB

Isopenicillin N synthase with substrate analogue ACOMP (35minutes oxygen exposure)

Summary for 2VBB

• Entry DOI: 10.2210/pdb2vbb/pdb
• Related: 1BK0 1BLZ 1HB1 1HB2 1HB3 1HB4 1IPS 1OBN 1OC1 1ODM 1ODN 1QIQ 1QJE 1QJF 1UZW 1W03 1W04 1W05 1W06 1W3V 1W3X 2BJS 2BU9 2IVI 2IVJ 2JB4 2VAU 2VBD 2VBP 2VCM 2VE1
• Descriptor: ISOPENICILLIN N SYNTHETASE, N^6^-{(1R)-2-{[(1S,2R)-1-carboxy-2-hydroxy-2-(methylsulfanyl)ethyl]oxy}-1-[(oxidosulfanyl)methyl]-2-oxoethyl}-6-oxo-L-lysine, FE (II) ION, ... (6 entities in total)
• Functional Keywords: oxidoreductase, antibiotic biosynthesis, penicillin biosynthesis, iron, oxygenase, vitamin c, metal-binding, monocyclic intermediate, b-lactam antibiotic
• 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: 38318.35

Authors

Ge, W.,Clifton, I.J.,Adlington, R.M.,Baldwin, J.E.,Rutledge, P.J. (deposition date: 2007-09-07, release date: 2008-07-29, Last modification date: 2024-05-08)

Primary citation

Ge, W.,Clifton, I.J.,Stok, J.E.,Adlington, R.M.,Baldwin, J.E.,Rutledge, P.J.
Isopenicillin N Synthase Mediates Thiolate Oxidation to Sulfenate in a Depsipeptide Substrate Analogue: Implications for Oxygen Binding and a Link to Nitrile Hydratase?
J.Am.Chem.Soc., 130:10096-, 2008

PubMed Abstract: Isopenicillin N synthase (IPNS) is a nonheme iron oxidase that catalyzes the central step in the biosynthesis of beta-lactam antibiotics: oxidative cyclization of the linear tripeptide delta-L-alpha-aminoadipoyl-L-cysteinyl-D-valine (ACV) to isopenicillin N (IPN). The ACV analogue delta-L-alpha-aminoadipoyl-L-cysteine (1-(S)-carboxy-2-thiomethyl)ethyl ester (ACOmC) has been synthesized as a mechanistic probe of IPNS catalysis and crystallized with the enzyme. The crystal structure of the anaerobic IPNS/Fe(II)/ACOmC complex was determined to 1.80 A resolution, revealing a highly congested active site region. By exposing these anaerobically grown crystals to high-pressure oxygen gas, an unexpected sulfenate product has been observed, complexed to iron within the IPNS active site. A mechanism is proposed for formation of the sulfenate-iron complex, and it appears that ACOmC follows a different reaction pathway at the earliest stages of its reaction with IPNS. Thus it seems that oxygen (the cosubstrate) binds in a different site to that observed in previous studies with IPNS, displacing a water ligand from iron in the process. The iron-mediated conversion of metal-bound thiolate to sulfenate has not previously been observed in crystallographic studies with IPNS. This mode of reactivity is of particular interest when considered in the context of another family of nonheme iron enzymes, the nitrile hydratases, in which post-translational oxidation of two cysteine thiolates to sulfenic and sulfinic acids is essential for enzyme activity.

PubMed: 18620394
DOI: 10.1021/JA8005397

Experimental method

X-RAY DIFFRACTION (1.4 Å)