3TKT

Crystal structure of CYP108D1 from Novosphingobium aromaticivorans DSM12444

Summary for 3TKT

• Entry DOI: 10.2210/pdb3tkt/pdb
• Descriptor: Cytochrome P450, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: cytochrome p450 fold, aromatic hydrocarbon binding of p450 enzyme, oxidoreductase
• Biological source: Novosphingobium aromaticivorans
• Total number of polymer chains: 1
• Total formula weight: 49964.62

Authors

Yang, W.,Bell, S.G.,Wang, H.,Zhou, W.,Bartlam, M.,Wong, L.-L.,Rao, Z. (deposition date: 2011-08-29, release date: 2012-02-29, Last modification date: 2023-11-01)

Primary citation

Bell, S.G.,Yang, W.,Yorke, J.A.,Zhou, W.,Wang, H.,Harmer, J.,Copley, R.,Zhang, A.,Zhou, R.,Bartlam, M.,Rao, Z.,Wong, L.-L.
Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme
Acta Crystallogr.,Sect.D, 68:277-291, 2012

PubMed 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.

PubMed: 22349230
DOI: 10.1107/S090744491200145X

Experimental method

X-RAY DIFFRACTION (2.2 Å)