NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol: Difference between revisions
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== The crystal structure of NADH quinone oxidoreductase (NQO1) in complex with its potent inhibitor dicoumarol == | == The crystal structure of NADH quinone oxidoreductase (NQO1) in complex with its potent inhibitor dicoumarol == | ||
[[Image:NQO_Dic copy.jpg|border|center|300px]] | |||
NAD(P)H quinone oxidoreductase 1 (NQO1) is a ubiquitous flavoenzyme that catalyzes two electron reduction of quinones to hydroquinones utilizing [[NAD(P)H]] as an electron donor. | NAD(P)H quinone oxidoreductase 1 (NQO1) is a ubiquitous flavoenzyme that catalyzes two electron reduction of quinones to hydroquinones utilizing [[NAD(P)H]] as an electron donor. | ||
NQO1 is a homo-dimer that functions via a “ping pong” mechanism. NAD(P)H binds to NQO1, reduces the [[FAD]] co-factor and is then released, allowing the quinone substrate to bind the enzyme and to be reduced. The NAD(P)H and the quinone binding sites of NQO1 have a significant overlap, thus providing a molecular basis for this “ping pong” mechanism. | NQO1 is a homo-dimer that functions via a “ping pong” mechanism. NAD(P)H binds to NQO1, reduces the [[FAD]] co-factor and is then released, allowing the quinone substrate to bind the enzyme and to be reduced. The NAD(P)H and the quinone binding sites of NQO1 have a significant overlap, thus providing a molecular basis for this “ping pong” mechanism. | ||
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The crystal structure of human NQO1 in complex with dicoumarol was determined at 2.75 Å resolution ([[2f1o]]). NQO1 is a <scene name='2f1o/Com_view/6'>physiological homodimer</scene> composed of two interlocked monomers. <scene name='2f1o/Com_view/7'>Two catalytic sites</scene> are formed and are present at the dimer interface (<font color='red'><b>FAD is colored red</b></font> and <font color='blue'><b>dicoumarol is colored blue</b></font>). Therefore, each from these two<scene name='2f1o/Active_site/3'>dicoumarol-hNQO1 binding sites</scene> is formed by both monomers. <font color='cyan'><b>Dicoumarol is colored cyan</b></font>, <font color='orange'><b>FAD in orange</b></font>, nitrogens and oxygens are shown in [http://en.wikipedia.org/wiki/CPK_coloring CPK colors]. NQO1 <font color='blueviolet'><b>chain A is colored blueviolet</b></font> and <font color='lime'><b>chain C in lime</b></font>. NQO1 residues, participating in ligand interactions, are shown as stick representation and are labeled (A and C refer to the NQO1 chains). H-bonds are shown by dashed lines with their distances. | The crystal structure of human NQO1 in complex with dicoumarol was determined at 2.75 Å resolution ([[2f1o]]). NQO1 is a <scene name='2f1o/Com_view/6'>physiological homodimer</scene> composed of two interlocked monomers. <scene name='2f1o/Com_view/7'>Two catalytic sites</scene> are formed and are present at the dimer interface (<font color='red'><b>FAD is colored red</b></font> and <font color='blue'><b>dicoumarol is colored blue</b></font>). Therefore, each from these two<scene name='2f1o/Active_site/3'>dicoumarol-hNQO1 binding sites</scene> is formed by both monomers. <font color='cyan'><b>Dicoumarol is colored cyan</b></font>, <font color='orange'><b>FAD in orange</b></font>, nitrogens and oxygens are shown in [http://en.wikipedia.org/wiki/CPK_coloring CPK colors]. NQO1 <font color='blueviolet'><b>chain A is colored blueviolet</b></font> and <font color='lime'><b>chain C in lime</b></font>. NQO1 residues, participating in ligand interactions, are shown as stick representation and are labeled (A and C refer to the NQO1 chains). H-bonds are shown by dashed lines with their distances. | ||
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<applet load='F1Ob.pdb' size='500' frame='true' align='left' scene='2f1o/Align/1' /> | |||
<scene name='2f1o/Align/8'>Structural comparison</scene> of the active site of <font color='magenta'><b>dicoumarol/hNQO1 complex</b></font> (residues important for ligand interactions are <font color='magenta'><b>colored magenta</b></font>) with that of <font color='blue'><b>apo hNQO1</b></font> dimer ([[1d4a]], residues important for ligand interactions are <font color='blue'><b>colored blue</b></font>) reveals that structural changes associated with dicoumarol binding occur on several residues involving both monomers. <font color='cyan'><b>Dicoumarol is colored in cyan</b></font>; <font color='orange'><b>FAD is colored in orange</b></font>. The RMSD between the apo hNQO1 ([[1d4a]]) and hNQO1 in complex with dicoumarol is 0.36Å for the 546 Cα atoms. The dicoumarol-hNQO1 binding causes several structural changes. The most prominent of them is Tyr 128 and Phe 232 movement in the first monomer. These residues are located on the surface of the NQO1 catalytic pocket. The <scene name='2f1o/Align/9'>distance</scene> between these residues increases from ~5 Å in the <font color='blue'><b>apo hNQO1</b></font> to ~12 Å in the <font color='magenta'><b>dicoumarol/hNQO1 complex</b></font>. | |||
Quinones (including duroquinone (2,3,5,6-tetramethyl-''p''-benzoquinone) are substrates of NQO1 (it catalyzes two-electron reduction of them to hydroquinones). Duroquinone <font color='black'><b>(yellow)</b></font> binds to the <scene name='2f1o/Align1/4'>active site</scene> by interactions involving the FAD and several hydrophobic and hydrophilic residues in the duroquinone-NQO1 complex ([[1dxo]]). The structure of the hNQO1 dimer in complex with duroquinone is also similar to that of hNQO1 in complex with dicoumarol (RMSD is 0.33Å for the 546 Cα atoms). In this case, the main differences between these two structures, as well as to that of apo hNQO1, involve the distance between residues <scene name='2f1o/Align1/5'>Tyr 128 and Phe 232</scene> of the first monomer. The FAD molecule has very similar conformation in both hNQO1-duroquinone <font color='pink'><b>(pink)</b></font> and hNQO1−dicoumarol <font color='orange'><b>(orange)</b></font> complexes. Based on the comparison of NQO1 structure in complex with different NQO1 inhibitors and our previous analysis of NQO1 mutations that affect NQO1 interactions we propose that the specific conformation of Tyr 128 and Phe 232 is important for NQO1 interaction with p53 and other client proteins. | |||
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The crystal structure of human <scene name='Nqo1/Nqo1_1/2'>NQO1</scene> in complex with dicoumarol was determine at 2.75 Å resolution. | The crystal structure of human <scene name='Nqo1/Nqo1_1/2'>NQO1</scene> in complex with dicoumarol was determine at 2.75 Å resolution. | ||
NQO1 is a physiological homodimer composed of two interlocked monomers. Each monomer is composed of two domains: a large catalytic domain with α/β fold with flavodoxin topology (residues 1-220) and a small C-terminal domain (residues 221-273). Two catalytic sites are formed and are present at the dimer interface. Two FAD molecules (red) are present; each one is bound to the catalytic domain of each monomer. The dicoumarol molecule (purple) is bound to each of the catalytic sites interacting with FAD and with residues from both monomer.The dicoumarol molecule is bound to each of the catalytic sites interacting with FAD and with residues from both monomers. | NQO1 is a physiological homodimer composed of two interlocked monomers. Each monomer is composed of two domains: a large catalytic domain with α/β fold with flavodoxin topology (residues 1-220) and a small C-terminal domain (residues 221-273). Two catalytic sites are formed and are present at the dimer interface. Two FAD molecules (red) are present; each one is bound to the catalytic domain of each monomer. The dicoumarol molecule (purple) is bound to each of the catalytic sites interacting with FAD and with residues from both monomer.The dicoumarol molecule is bound to each of the catalytic sites interacting with FAD and with residues from both monomers. | ||
Structural comparison of the apo hNQO1 dimer (PDB accession code 1D4A in cyan) with hNQO1 in complex with dicoumarol(pink) reveals that structural changes associated with dicoumarol binding occur on several residues involving both monomers. The most prominent conformational changes that occur in the presence of dicoumarol involve Tyr 128 and Phe 232 that are present on the surface of the NQO1 catalytic pocket. Based on the comparison of NQO1 structure in complex with different NQO1 inhibitors and our previous analysis of NQO1 mutations that affect NQO1 interactions we propose that the specific conformation of Tyr 128 and Phe 232 is important for NQO1 interaction with p53 and other client proteins. | Structural comparison of the apo hNQO1 dimer (PDB accession code 1D4A in cyan) with hNQO1 in complex with dicoumarol(pink) reveals that structural changes associated with dicoumarol binding occur on several residues involving both monomers. The most prominent conformational changes that occur in the presence of dicoumarol involve Tyr 128 and Phe 232 that are present on the surface of the NQO1 catalytic pocket. Based on the comparison of NQO1 structure in complex with different NQO1 inhibitors and our previous analysis of NQO1 mutations that affect NQO1 interactions we propose that the specific conformation of Tyr 128 and Phe 232 is important for NQO1 interaction with p53 and other client proteins. | ||
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[[Image:Slide1.jpg|border|center|300px]] | [[Image:Slide1.jpg|border|center|300px]] | ||
