title: Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme.
abstract: CYP108D1 from Novosphingobium aromaticivorans DSM12444 binds a range of aromatic hydrocarbons such as phenanthrene, biphenyl and phenylcyclohexane. Its structure, which is reported here at 2.2 Å resolution, is closely related to that of CYP108A1 (P450terp), an α-terpineol-oxidizing enzyme. The compositions and structures of the active sites of these two enzymes are very similar; the most significant changes are the replacement of Glu77 and Thr103 in CYP108A1 by Thr79 and Val105 in CYP108D1. Other residue differences lead to a larger and more hydrophobic access channel in CYP108D1. These structural features are likely to account for the weaker α-terpineol binding by CYP108D1 and, when combined with the presence of three hydrophobic phenylalanine residues in the active site, promote the binding of aromatic hydrocarbons. The haem-proximal surface of CYP108D1 shows a different charge distribution and topology to those of CYP101D1, CYP101A1 and CYP108A1, including a pronounced kink in the proximal loop of CYP108D1, which may result in poor complementarity with the [2Fe-2S] ferredoxins Arx, putidaredoxin and terpredoxin that are the respective redox partners of these three P450 enzymes. The unexpectedly low reduction potential of phenylcyclohexane-bound CYP108D1 (-401 mV) may also contribute to the low activity observed with these ferredoxins. CYP108D1 appears to function as an aromatic hydrocarbon hydroxylase that requires a different electron-transfer cofactor protein.
authors.affiliation: Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford,South Parks Road, Oxford OX1 3QR, England. stephen.bell@chem.ox.ac.uk
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Bell
authors.forename: Wen
authors.initials: W
authors.lastname: Yang
authors.forename: Jake A
authors.initials: JA
authors.lastname: Yorke
authors.forename: Weihong
authors.initials: W
authors.lastname: Zhou
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Harmer
authors.forename: Rachel
authors.initials: R
authors.lastname: Copley
authors.forename: Aili
authors.initials: A
authors.lastname: Zhang
authors.forename: Ruimin
authors.initials: R
authors.lastname: Zhou
authors.forename: Mark
authors.initials: M
authors.lastname: Bartlam
authors.forename: Zihe
authors.initials: Z
authors.lastname: Rao
authors.forename: Luet Lok
authors.initials: LL
authors.lastname: Wong
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000502:physiology; D055162:Biocatalysis; D001673:Biodegradation, Environmental; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D005288:Ferredoxins / Q000737:chemistry* / Q000378:metabolism; D006841:Hydrocarbons, Aromatic / Q000737:chemistry*; D017433:Protein Structure, Secondary; D042301:Sphingomonadaceae / Q000201:enzymology* / Q000378:metabolism; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D005288:Ferredoxins; D006841:Hydrocarbons, Aromatic; D003577:Cytochrome P-450 Enzyme System; C574592:CYP108D1, Novosphingobium aromaticivorans