1W04

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

Summary for 1W04

• Entry DOI: 10.2210/pdb1w04/pdb
• Related: 1BK0 1BLZ 1HB1 1HB2 1HB3 1HB4 1IPS 1OBN 1OC1 1ODM 1ODN 1QIQ 1QJE 1QJF 1UZW 1W03 1W05 1W06
• Descriptor: ISOPENICILLIN N SYNTHETASE, DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-GLYCINE, FE (II) ION, ... (6 entities in total)
• Functional Keywords: oxidoreductase, b-lactam antibiotic, 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: 38166.19

Authors

Long, A.J.,Clifton, I.J.,Rutledge, P.J. (deposition date: 2004-06-01, release date: 2005-05-04, Last modification date: 2024-05-08)

Primary citation

Long, A.J.,Clifton, I.J.,Roach, P.L.,Baldwin, J.E.,Schofield, C.J.,Rutledge, P.J.
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
Biochemistry, 44:6619-, 2005

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.

PubMed: 15850395
DOI: 10.1021/BI047478Q

Experimental method

X-RAY DIFFRACTION (1.28 Å)