PDBsum entry 1hb1

Antibiotic biosynthesis

PDB id: 1hb1

Contents

Protein chain

328 a.a. *

Ligands

OCV

SO4

Metals

FE2

Waters ×288

* Residue conservation analysis

PDB id:

1hb1

Name:

Antibiotic biosynthesis

Title:

Isopenicillin n synthase from aspergillus nidulans (anaerobic acov fe complex)

Structure:

Isopenicillin n synthase. Chain: a. Engineered: yes

Source:

Emericella nidulans (strain fgsc a4 / atcc 38163 / cbs 112.46 / nrrl 194 / m139). Aspergillus nidulans. Organism_taxid: 227321. Gene: pcb c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.55Å R-factor: 0.184 R-free: 0.204

Authors:

J.M.Ogle,I.J.Clifton,P.J.Rutledge,J.M.Elkins,N.I.Burzlaff, R.M.Adlington,P.L.Roach,J.E.Baldwin

Key ref:

J.M.Ogle et al. (2001). Alternative oxidation by isopenicillin N synthase observed by X-ray diffraction. Chem Biol, 8, 1231-1237. PubMed id: 11755401 DOI: 10.1016/S1074-5521(01)00090-4

Date:

11-Apr-01 Release date: 23-Nov-01

Protein chain

P05326  (IPNS_EMENI) -  Isopenicillin N synthase from Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)

Seq: 331 a.a.

Struc: 328 a.a.

Enzyme reactions

• Enzyme class: E.C.1.21.3.1 - isopenicillin-N synthase.
• Pathway: Penicillin N and Deacetoxycephalosporin C Biosynthesis
• Reaction: N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + O2 = isopenicillin N + 2 H2O

N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine + O2 = isopenicillin N + 2 × H2O (Bound ligand (Het Group name = OCV) matches with 50.00% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/S1074-5521(01)00090-4

Chem Biol 8:1231-1237 (2001)

PubMed id: 11755401

Alternative oxidation by isopenicillin N synthase observed by X-ray diffraction.

J.M.Ogle, I.J.Clifton, P.J.Rutledge, J.M.Elkins, N.I.Burzlaff, R.M.Adlington, P.L.Roach, J.E.Baldwin.

ABSTRACT

BACKGROUND: Isopenicillin N synthase (IPNS) catalyses formation of bicyclic isopenicillin N, precursor to all penicillin and cephalosporin antibiotics, from the linear tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine. IPNS is a non-haem iron(II)-dependent enzyme which utilises the full oxidising potential of molecular oxygen in catalysing the bicyclisation reaction. The reaction mechanism is believed to involve initial formation of the beta-lactam ring (via a thioaldehyde intermediate) to give an iron(IV)-oxo species, which then mediates closure of the 5-membered thiazolidine ring. RESULTS: Here we report experiments employing time-resolved crystallography to observe turnover of an isosteric substrate analogue designed to intercept the catalytic pathway at an early stage. Reaction in the crystalline enzyme-substrate complex was initiated by the application of high-pressure oxygen, and subsequent flash freezing allowed an oxygenated product to be trapped, bound at the iron centre. A mechanism for formation of the observed thiocarboxylate product is proposed. CONCLUSIONS: In the absence of its natural reaction partner (the N-H proton of the L-cysteinyl-D-valine amide bond), the proposed hydroperoxide intermediate appears to attack the putative thioaldehyde species directly. These results shed light on the events preceding beta-lactam closure in the IPNS reaction cycle, and enhance our understanding of the mechanism for reaction of the enzyme with its natural substrate.

Selected figure(s)

Figure 1.
Fig. 1. Mechanisms for the reaction of IPNS with ACV and ACOV. (a) Proposed mechanism for the reaction of IPNS with its natural substrate ACV [3]. (b) Proposed pathway for generation of the thiocarboxylate product from the substrate analogue ACOV. See text for details of compounds 1–10. AA, δ-( Image -α-aminoadipoyl).

Figure 4.
Fig. 4. Potential hydrogen bonding interactions in the active site region of the exposed IPNS:Fe(II):ACOV structure. The three exposed structures oriented to show the potential for hydrogen bonding around the thiocarboxylate oxygen, and to demonstrate the consistency of the thiocarboxylate electron density across the three structures. (a) From the 1.30 Å resolution structure in the plane of the thiocarboxylate, showing distances to Wat 402 and Wat 403. (b) The 1.30 Å 30 s, (c) the 1.40 Å 30 s, and (d) the 1.50 Å 120 s structures from an alternative angle.

The above figures are reprinted by permission from Cell Press: Chem Biol (2001, 8, 1231-1237) copyright 2001.

Figures were selected by an automated process.