2Y6F

Isopenicillin N synthase with AC-D-S-methyl-3R-methylcysteine

Summary for 2Y6F

• Entry DOI: 10.2210/pdb2y6f/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 2VBB 2VBD 2VBP 2VCM 2VE1 2WO7 2Y60
• Descriptor: ISOPENICILLIN N SYNTHASE, (2S)-2-AMINO-6-[[(2R)-1-[[(2S)-1-HYDROXY-3-METHYLSULFANYL-1-OXO-BUTAN-2-YL]AMINO]-1-OXO-3-SULFANYL-PROPAN-2-YL]AMINO]-6-OXO-HEXANOIC ACID, FE (III) ION, ... (5 entities in total)
• Functional Keywords: 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: 38111.24

Authors

Rutledge, P.J.,Clifton, I.J.,Ge, W. (deposition date: 2011-01-21, release date: 2011-08-31, Last modification date: 2024-05-08)

Primary citation

Clifton, I.J.,Ge, W.,Adlington, R.M.,Baldwin, J.E.,Rutledge, P.J.
Isopenicillin N Synthase Binds Delta-(L-Alpha-Aminoadipoyl)-L-Cysteinyl-D-Thia-Allo-Isoleucine Through Both Sulfur Atoms.
Chembiochem, 12:1881-, 2011

PubMed Abstract: Isopenicillin N synthase (IPNS) catalyses the synthesis of isopenicillin N (IPN), the biosynthetic precursor to penicillin and cephalosporin antibiotics. IPNS is a non-heme iron(II) oxidase that mediates the oxidative cyclisation of the tripeptide δ-L-α-aminoadipoyl-L-cysteinyl-D-valine (ACV) to IPN with a concomitant reduction of molecular oxygen to water. Solution-phase incubation experiments have shown that, although IPNS can turn over analogues with a diverse range of hydrocarbon side chains in the third (valinyl) position of its substrate, the enzyme is much less tolerant of polar residues in this position. Thus, although IPNS converts δ-L-α-aminoadipoyl-L-cysteinyl-D-isoleucine (ACI) and AC-D-allo-isoleucine (ACaI) to penam products, the isosteric sulfur-containing peptides AC-D-thiaisoleucine (ACtI) and AC-D-thia-allo-isoleucine (ACtaI) are not turned over. To determine why these peptides are not substrates, we crystallized ACtaI with IPNS. We report the synthesis of ACtaI and the crystal structure of the IPNS:Fe(II) :ACtaI complex to 1.79 Å resolution. This structure reveals direct ligation of the thioether side chain to iron: the sulfide sulfur sits 2.66 Å from the metal, squarely in the oxygen binding site. This result articulates a structural basis for the failure of IPNS to turn over these substrates.

PubMed: 21678539
DOI: 10.1002/CBIC.201100149

Experimental method

X-RAY DIFFRACTION (1.79 Å)