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The crystal structure of an isopenicillin N synthase complex with an ethereal substrate analogue reveals water in the oxygen binding site
Author(s) -
Clifton Ian J.,
Ge Wei,
Adlington Robert M.,
Baldwin Jack E.,
Rutledge Peter J.
Publication year - 2013
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2013.07.016
Subject(s) - stereochemistry , tripeptide , chemistry , active site , ether , substrate (aquarium) , hydrogen bond , residue (chemistry) , crystal structure , molecule , substrate analog , moiety , enzyme , crystallography , organic chemistry , amino acid , biochemistry , biology , ecology
Isopenicillin N synthase (IPNS) is a non‐heme iron oxidase central to the biosynthesis of β‐lactam antibiotics. IPNS converts the tripeptide δ‐( l ‐α‐aminoadipoyl)‐ l ‐cysteinyl‐ d ‐valine (ACV) to isopenicillin N while reducing molecular oxygen to water. The substrate analogue δ‐( l ‐α‐aminoadipoyl)‐ l ‐cysteinyl‐ O ‐methyl‐ d ‐threonine (ACmT) is not turned over by IPNS. Epimeric δ‐( l ‐α‐aminoadipoyl)‐ l ‐cysteinyl‐ O ‐methyl‐ d ‐ allo ‐threonine (ACm a T) is converted to a bioactive penam product. ACmT and ACm a T differ from each other only in the stereochemistry at the β‐carbon atom of their third residue. These substrates both contain a methyl ether in place of the isopropyl group of ACV. We report an X‐ray crystal structure for the anaerobic IPNS:Fe(II):ACmT complex. This structure reveals an additional water molecule bound to the active site metal, held by hydrogen‐bonding to the ether oxygen atom of the substrate analogue.