5EM4

Structure of CYP2B4 F244W in a ligand free conformation

Summary for 5EM4

• Entry DOI: 10.2210/pdb5em4/pdb
• Related: 1PO5 1SUO 2BDM 2Q6N 3G5N 3G93 3KW4 3ME6 3MVR 3R1A 3R1B 3TK3 3TMZ 3UAS 4H1N 4JLT
• Descriptor: Cytochrome P450 2B4, PROTOPORPHYRIN IX CONTAINING FE, 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE, ... (4 entities in total)
• Functional Keywords: cytochrome p450, monooxygenase, oxidoreductase
• Biological source: Oryctolagus cuniculus (Rabbit)
• Total number of polymer chains: 2
• Total formula weight: 115109.98

Authors

Shah, M.B.,Stout, C.D.,Halpert, J.R. (deposition date: 2015-11-05, release date: 2016-03-23, Last modification date: 2023-09-27)

Primary citation

Liu, J.,Shah, M.B.,Zhang, Q.,Stout, C.D.,Halpert, J.R.,Wilderman, P.R.
Coumarin Derivatives as Substrate Probes of Mammalian Cytochromes P450 2B4 and 2B6: Assessing the Importance of 7-Alkoxy Chain Length, Halogen Substitution, and Non-Active Site Mutations.
Biochemistry, 55:1997-2007, 2016

PubMed Abstract: Using a combined structural and biochemical approach, the functional importance of a recently described peripheral pocket bounded by the E-, F-, G-, and I-helices in CYP2B4 and 2B6 was probed. Three series of 4-substituted-7-alkoxycoumarin derivatives with -H, -CH3, or -CF3 at the 4 position of the coumarin core were used initially to monitor functional differences between CYP2B4 and 2B6. 7-Ethoxy-4-(trifluoromethyl)coumarin (7-EFC) displayed the highest catalytic efficiency among these substrates. Mutants were made to alter side-chain polarity (V/E194Q) or bulk (F/Y244W) to alter access to the peripheral pocket. Modest increases in catalytic efficiency of 7-EFC O-deethylation by the mutants were magnified considerably by chlorination or bromination of the substrate ethoxy chain. A structure of CYP2B6 Y244W in complex with (+)-α-pinene was solved at 2.2 Å and showed no CYMAL-5 in the peripheral pocket. A ligand free structure of CYP2B4 F244W was solved at 3.0 Å with CYMAL-5 in the peripheral pocket. In both instances, comparison of the respective wild-type and mutant CYP2B enzymes revealed that CYMAL-5 occupancy of the peripheral pocket had little effect on the topology of active site residue side-chains, despite the fact that the peripheral pocket and active site are located on opposite sides of the I-helix. Analysis of available CYP2B structures suggest that the effect of the amino acid substitutions within the peripheral pocket derive from altered interactions between the F and G helices.

PubMed: 26982502
DOI: 10.1021/acs.biochem.5b01330

Experimental method

X-RAY DIFFRACTION (3.02 Å)