Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode.
Human microsomal cytochrome P450 (CYP) 2E1 is widely known for its ability to oxidize >70 different, mostly compact, low molecular weight drugs and other xenobiotic compounds. In addition CYP2E1 oxidizes much larger C9-C20 fatty acids that can serve as endogenous signaling molecules. Previously structures of CYP2E1 with small molecules revealed a small, compact CYP2E1 active site, which would be insufficient to accommodate medium and long chain fatty acids without conformational changes in the protein. In the current work we have determined how CYP2E1 can accommodate a series of fatty acid analogs by cocrystallizing CYP2E1 with omega-imidazolyl-octanoic fatty acid, omega-imidazolyl-decanoic fatty acid, and omega-imidazolyl-dodecanoic fatty acid. In each structure direct coordination of the imidazole nitrogen to the heme iron mimics the position required for native fatty acid substrates to yield the omega-1 hydroxylated metabolites that predominate experimentally. In each case rotation of a single Phe(298) side chain merges the active site with an adjacent void, significantly altering the active site size and topology to accommodate fatty acids. The binding of these fatty acid ligands is directly opposite the channel to the protein surface and the binding observed for fatty acids in the bacterial cytochrome P450 BM3 (CYP102A1) from Bacillus megaterium. Instead of the BM3-like binding mode in the CYP2E1 channel, these structures reveal interactions between the fatty acid carboxylates and several residues in the F, G, and B' helices at successive distances from the active site.
Porubsky
Patrick R
PR
Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, USA.
Battaile
Kevin P
KP
Scott
Emily E
EE
D018360:Crystallography, X-Ray; D019392:Cytochrome P-450 CYP2E1 / Q000737:chemistry* / Q000378:metabolism*; D005227:Fatty Acids / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012984:Software
D005227:Fatty Acids; D008024:Ligands; D019392:Cytochrome P-450 CYP2E1
Nature. 1996 May 23;381(6580):272
8692262
Circ Res. 2000 Jul 7;87(1):60-5
10884373
Biochemistry. 2001 Nov 13;40(45):13456-65
11695892
Methods Enzymol. 1997;276:307-26
27754618
J Biol Chem. 2003 Mar 14;278(11):9761-7
12519760
J Biol Chem. 2008 Nov 28;283(48):33698-707
18818195
Arch Biochem Biophys. 1997 Jan 1;337(1):1-7
8990261
Toxicol Appl Pharmacol. 2000 Nov 1;168(3):268-79
11042099
Fundam Clin Pharmacol. 1998;12(5):553-8
9794154
Nat Struct Biol. 1997 Feb;4(2):140-6
9033595
Biochem J. 2005 Sep 15;390(Pt 3):719-27
15916533
J Biochem. 1994 Feb;115(2):338-44
8206883
Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):72-82
16369096
Toxicol Appl Pharmacol. 1998 Sep;152(1):276-81
9772223
J Lipid Res. 1999 Nov;40(11):1990-7
10553002
Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55
15299926
Biochemistry. 2000 May 16;39(19):5731-7
10801323
J Biol Chem. 1993 Jun 15;268(17):12912-8
8509425
Am J Physiol. 1999 Sep;277(3):R607-23
10484476
Biochemistry. 2008 Mar 25;47(12):3662-70
18298086
BMC Bioinformatics. 2006 Jun 22;7:316
16792811
J Comb Chem. 2001 Mar-Apr;3(2):205-15
11300862
Proc Natl Acad Sci U S A. 2008 Oct 14;105(41):15696-701
18838690
Org Biomol Chem. 2005 Aug 7;3(15):2688-90
16032346
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
15572765
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
19461840
Arch Biochem Biophys. 1995 Jul 10;320(2):289-96
7625836
Am J Physiol. 1996 Oct;271(4 Pt 2):R863-9
8897975
Acta Crystallogr D Biol Crystallogr. 1994 Mar 1;50(Pt 2):178-85
15299456