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Rabe P, Walla CC, Goodyear NK, Welsh J, Southwart R, Clifton I, Linyard JDS, Tumber A, Claridge TDW, Myers WK, Schofield CJ. Spectroscopic studies reveal details of substrate-induced conformational changes distant from the active site in isopenicillin N synthase. J Biol Chem 2022; 298:102249. [PMID: 35835215 PMCID: PMC9403350 DOI: 10.1016/j.jbc.2022.102249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/06/2022] Open
Abstract
Isopenicillin N synthase (IPNS) catalyzes formation of the β-lactam and thiazolidine rings of isopenicillin N from its linear tripeptide l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) substrate in an iron- and dioxygen (O2)-dependent four-electron oxidation without precedent in current synthetic chemistry. Recent X-ray free-electron laser studies including time-resolved serial femtosecond crystallography show that binding of O2 to the IPNS–Fe(II)–ACV complex induces unexpected conformational changes in α-helices on the surface of IPNS, in particular in α3 and α10. However, how substrate binding leads to conformational changes away from the active site is unknown. Here, using detailed 19F NMR and electron paramagnetic resonance experiments with labeled IPNS variants, we investigated motions in α3 and α10 induced by binding of ferrous iron, ACV, and the O2 analog nitric oxide, using the less mobile α6 for comparison. 19F NMR studies were carried out on singly and doubly labeled α3, α6, and α10 variants at different temperatures. In addition, double electron–electron resonance electron paramagnetic resonance analysis was carried out on doubly spin-labeled variants. The combined spectroscopic and crystallographic results reveal that substantial conformational changes in regions of IPNS including α3 and α10 are induced by binding of ACV and nitric oxide. Since IPNS is a member of the structural superfamily of 2-oxoglutarate-dependent oxygenases and related enzymes, related conformational changes may be of general importance in nonheme oxygenase catalysis.
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Affiliation(s)
- Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
| | - Carla C Walla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Noelle K Goodyear
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jordan Welsh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom; Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Rebecca Southwart
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ian Clifton
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - James D S Linyard
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - William K Myers
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
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Abstract
Metabolic engineering has become a rational alternative to classical strain improvement in optimisation of beta-lactam production. In metabolic engineering directed genetic modification are introduced to improve the cellular properties of the production strains. This has resulted in substantial increases in the existing beta-lactam production processes. Furthermore, pathway extension, by heterologous expression of novel genes in well-characterised strains, has led to introduction of new fermentation processes that replace environmentally damaging chemical methods. This minireview discusses the recent developments in metabolic engineering and the applications of this approach for improving beta-lactam production.
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Affiliation(s)
- Jette Thykaer
- Center for Process Biotechnology, BioCentrum, Technical University of Denmark, Building 223, DK-2800, Lyngby, Denmark
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Dubus A, Sami M, Brown TJ, Schofield CJ, Baldwin JE, Frère JM. Studies of isopenicillin N synthase enzymatic properties using a continuous spectrophotometric assay. FEBS Lett 2000; 485:142-6. [PMID: 11094156 DOI: 10.1016/s0014-5793(00)02221-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isopenicillin N synthase (IPNS) from Aspergillus nidulans is a no-heme iron(II)-dependent oxygenase which catalyses, in a single reaction, the bicyclisation of delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine into isopenicillin N, the precursor of all other penicillins, cephalosporins and cephamycins. The IPNS reaction can be followed directly and continuously by a new assay which monitors the absorbance increase at 235 nm characteristic of penicillin nucleus formation. Using this assay, the effects of influential factors affecting the in vitro IPNS enzymatic reaction were investigated. Even under optimal conditions, enzyme inactivation occurred during catalysis. Iron(II) depletion and product inhibition were not the cause of this phenomenon, the addition of antioxidants or reducing agents failed to slow down inactivation or reactivate the enzyme. Therefore, this phenomenon appears to be irreversible and is attributed to oxidative damage caused to the enzyme by reactive oxygen species generated in solution during catalysis. Nevertheless, the steady-state kinetic parameters for the IPNS reaction were determined.
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Affiliation(s)
- A Dubus
- Laboratoire d'Enzymologie, CIP, Institut di Chimie B6, University of Liège, Belgium.
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Baldwin JE, Adlington RM, C. Crabbe M, Nomoto T, Schofield CJ. An efficient substitute for the α-amimoadipoyl moiety of δ-(-α-aminloadipoytl)--cisteintl--valine in the emzymatic synthesis of penicillins. Tetrahedron 1987. [DOI: 10.1016/s0040-4020(01)83463-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Baldwin JE, Gagnon J, Ting H. N-terminal amino acid sequence and some properties of isopenicillin-N synthetase from Cephalosporium acremonium. FEBS Lett 1985; 188:253-6. [PMID: 3839755 DOI: 10.1016/0014-5793(85)80382-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Isopenicillin-N synthetase (IPNS) was purified to homogeneity from Cephalosporium acremonium C0728. The enzyme existed in two states during purification; an oxidised state with a disulphide linkage and its reduced state. These two forms can be interconverted in the presence or absence of thiol agents, and separated by fast protein liquid chromatography (FPLC) with the strong anion exchange Mono-Q column. The enzyme is a monomer with a molecular mass of 38 kDa and pI 5.05. The first 50 amino acid N-terminal sequence of the enzyme was determined. The purified enzyme has an absolute requirement of Fe2+ and a 2-electron donor for activity.
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