2bdm: Difference between revisions

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~~[[Image:2bdm.gif|left|200px]]<br /><applet load="2bdm" size="450" color="white" frame="true" align="right" spinBox="true"~~

~~caption="2bdm, resolution 2.300Å" />~~

~~'''Structure of Cytochrome P450 2B4 with Bound Bifonazole'''<br />~~

==~~Overview~~==

==Structure of Cytochrome P450 2B4 with Bound Bifonazole==

To better understand ligand-induced structural transitions in cytochrome, P450 2B4, protein-ligand interactions were investigated using a bulky, inhibitor. Bifonazole, a broad spectrum antifungal agent, inhibits, monooxygenase activity and induces a type II binding spectrum in, 2B4dH(H226Y), a modified enzyme previously crystallized in the presence of, 4-(4-chlorophenyl)imidazole (CPI). Isothermal titration calorimetry and, tryptophan fluorescence quenching indicate no significant burial of, protein apolar surface nor altered accessibility of Trp-121 upon, bifonazole binding, in contrast to recent results with CPI. A 2.3 A, crystal structure of 2B4-bifonazole reveals a novel open conformation with, ligand bound in the active site, which is significantly different from, either the U-shaped cleft of ligand-free 2B4 or the small active site, pocket of 2B4-CPI. The O-shaped active site cleft of 2B4-bifonazole is, widely open in the middle but narrow at the top. A bifonazole molecule, occupies the bottom of the active site cleft, where helix I is bent, approximately 15 degrees to accommodate the bulky ligand. The structure, also defines unanticipated interactions between helix C residues and, bifonazole, suggesting an important role of helix C in azole recognition, by mammalian P450s. Comparison of the ligand-free 2B4 structure, the, 2B4-CPI structure, and the 2B4-bifonazole structure identifies, structurally plastic regions that undergo correlated conformational, changes in response to ligand binding. The most plastic regions are, putative membrane-binding motifs involved in substrate access or substrate, binding. The results allow us to model the membrane-associated state of, P450 and provide insight into how lipophilic substrates access the buried, active site.

== Structural highlights ==

<table><tr><td colspan='2'>[[2bdm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BDM FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CM5:5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE'>CM5</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=TMI:1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE'>TMI</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdm OCA], [https://pdbe.org/2bdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bdm RCSB], [https://www.ebi.ac.uk/pdbsum/2bdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bdm ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/CP2B4_RABIT CP2B4_RABIT] Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. In the epoxidation of arachidonic acid it has a unique preference for the 5,6-olefin.

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bd/2bdm_consurf.spt"</scriptWhenChecked>

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>

<text>to colour the structure by Evolutionary Conservation</text>

</jmolCheckbox>

</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2bdm ConSurf].

== Publication Abstract from PubMed ==

To better understand ligand-induced structural transitions in cytochrome P450 2B4, protein-ligand interactions were investigated using a bulky inhibitor. Bifonazole, a broad spectrum antifungal agent, inhibits monooxygenase activity and induces a type II binding spectrum in 2B4dH(H226Y), a modified enzyme previously crystallized in the presence of 4-(4-chlorophenyl)imidazole (CPI). Isothermal titration calorimetry and tryptophan fluorescence quenching indicate no significant burial of protein apolar surface nor altered accessibility of Trp-121 upon bifonazole binding, in contrast to recent results with CPI. A 2.3 A crystal structure of 2B4-bifonazole reveals a novel open conformation with ligand bound in the active site, which is significantly different from either the U-shaped cleft of ligand-free 2B4 or the small active site pocket of 2B4-CPI. The O-shaped active site cleft of 2B4-bifonazole is widely open in the middle but narrow at the top. A bifonazole molecule occupies the bottom of the active site cleft, where helix I is bent approximately 15 degrees to accommodate the bulky ligand. The structure also defines unanticipated interactions between helix C residues and bifonazole, suggesting an important role of helix C in azole recognition by mammalian P450s. Comparison of the ligand-free 2B4 structure, the 2B4-CPI structure, and the 2B4-bifonazole structure identifies structurally plastic regions that undergo correlated conformational changes in response to ligand binding. The most plastic regions are putative membrane-binding motifs involved in substrate access or substrate binding. The results allow us to model the membrane-associated state of P450 and provide insight into how lipophilic substrates access the buried active site.

~~==About this~~ Structure==

Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.,Zhao Y, White MA, Muralidhara BK, Sun L, Halpert JR, Stout CD J Biol Chem. 2006 Mar 3;281(9):5973-81. Epub 2005 Dec 21. PMID:16373351<ref>PMID:16373351</ref>

~~2BDM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure~~ of ~~sequence from [http~~:~~//en~~.~~wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with HEM~~, ~~TMI and CM5 as [http://en.wikipedia~~.~~org/wiki/ligands ligands]. Active as [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Unspecific_monooxygenase Unspecific monooxygenase], with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.1 1.14.14.1] Full crystallographic information is available from [http~~:/~~/ispc.weizmann.ac.il/oca-bin/ocashort?id=2BDM OCA].~~

==~~Reference~~==

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

~~Structure of microsomal cytochrome~~ P450 ~~2B4 complexed with the antifungal drug bifonazole: insight into~~ P450 ~~conformational plasticity and membrane interaction., Zhao Y, White MA, Muralidhara BK, Sun L, Halpert JR, Stout CD, J Biol Chem. 2006 Mar 3;281(9):5973-81. Epub 2005 Dec 21. PMID:~~[~~http~~:~~//ispc.weizmann.ac.il//pmbin/getpm?pmid=16373351 16373351~~]

</div>

==See Also==

*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Oryctolagus cuniculus]]

~~[[Category: Single protein]]~~

[[Category: Halpert JR]]

~~[[Category: Unspecific monooxygenase]]~~

[[Category: Muralidhara BK]]

[[Category: Halpert~~, J.R.~~]]

[[Category: Stout CD]]

[[Category: Muralidhara~~, B.K.~~]]

[[Category: Sun L]]

[[Category: Stout~~, C.D.~~]]

[[Category: White MA]]

[[Category: Sun, L.]]

[[Category: Zhao Y]]

[[Category: White~~, M.A.~~]]

[[Category: Zhao, Y~~.]]~~

~~[[Category: CM5]]~~

~~[[Category: HEM]]~~

~~[[Category: TMI]]~~

~~[[Category: cyp 2b4]]~~

~~[[Category: cyp lm2]]~~

~~[[Category: membrane protein]]~~

~~[[Category: monooxygenase]~~]

~~[[Category: oxidoreductase~~]]

~~[[Category: p450]]~~

~~''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:44:50 2007''~~

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@@ Line 1: / Line 1: @@
-[[Image:2bdm.gif|left|200px]]<br /><applet load="2bdm" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2bdm, resolution 2.300&Aring;" />
-'''Structure of Cytochrome P450 2B4 with Bound Bifonazole'''<br />
-==Overview==
+==Structure of Cytochrome P450 2B4 with Bound Bifonazole==
-To better understand ligand-induced structural transitions in cytochrome, P450 2B4, protein-ligand interactions were investigated using a bulky, inhibitor. Bifonazole, a broad spectrum antifungal agent, inhibits, monooxygenase activity and induces a type II binding spectrum in, 2B4dH(H226Y), a modified enzyme previously crystallized in the presence of, 4-(4-chlorophenyl)imidazole (CPI). Isothermal titration calorimetry and, tryptophan fluorescence quenching indicate no significant burial of, protein apolar surface nor altered accessibility of Trp-121 upon, bifonazole binding, in contrast to recent results with CPI. A 2.3 A, crystal structure of 2B4-bifonazole reveals a novel open conformation with, ligand bound in the active site, which is significantly different from, either the U-shaped cleft of ligand-free 2B4 or the small active site, pocket of 2B4-CPI. The O-shaped active site cleft of 2B4-bifonazole is, widely open in the middle but narrow at the top. A bifonazole molecule, occupies the bottom of the active site cleft, where helix I is bent, approximately 15 degrees to accommodate the bulky ligand. The structure, also defines unanticipated interactions between helix C residues and, bifonazole, suggesting an important role of helix C in azole recognition, by mammalian P450s. Comparison of the ligand-free 2B4 structure, the, 2B4-CPI structure, and the 2B4-bifonazole structure identifies, structurally plastic regions that undergo correlated conformational, changes in response to ligand binding. The most plastic regions are, putative membrane-binding motifs involved in substrate access or substrate, binding. The results allow us to model the membrane-associated state of, P450 and provide insight into how lipophilic substrates access the buried, active site.
+<StructureSection load='2bdm' size='340' side='right'caption='[[2bdm]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2bdm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BDM FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CM5:5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE'>CM5</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=TMI:1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE'>TMI</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bdm OCA], [https://pdbe.org/2bdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bdm RCSB], [https://www.ebi.ac.uk/pdbsum/2bdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bdm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CP2B4_RABIT CP2B4_RABIT] Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. In the epoxidation of arachidonic acid it has a unique preference for the 5,6-olefin.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bd/2bdm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2bdm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+To better understand ligand-induced structural transitions in cytochrome P450 2B4, protein-ligand interactions were investigated using a bulky inhibitor. Bifonazole, a broad spectrum antifungal agent, inhibits monooxygenase activity and induces a type II binding spectrum in 2B4dH(H226Y), a modified enzyme previously crystallized in the presence of 4-(4-chlorophenyl)imidazole (CPI). Isothermal titration calorimetry and tryptophan fluorescence quenching indicate no significant burial of protein apolar surface nor altered accessibility of Trp-121 upon bifonazole binding, in contrast to recent results with CPI. A 2.3 A crystal structure of 2B4-bifonazole reveals a novel open conformation with ligand bound in the active site, which is significantly different from either the U-shaped cleft of ligand-free 2B4 or the small active site pocket of 2B4-CPI. The O-shaped active site cleft of 2B4-bifonazole is widely open in the middle but narrow at the top. A bifonazole molecule occupies the bottom of the active site cleft, where helix I is bent approximately 15 degrees to accommodate the bulky ligand. The structure also defines unanticipated interactions between helix C residues and bifonazole, suggesting an important role of helix C in azole recognition by mammalian P450s. Comparison of the ligand-free 2B4 structure, the 2B4-CPI structure, and the 2B4-bifonazole structure identifies structurally plastic regions that undergo correlated conformational changes in response to ligand binding. The most plastic regions are putative membrane-binding motifs involved in substrate access or substrate binding. The results allow us to model the membrane-associated state of P450 and provide insight into how lipophilic substrates access the buried active site.
-==About this Structure==
+Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.,Zhao Y, White MA, Muralidhara BK, Sun L, Halpert JR, Stout CD J Biol Chem. 2006 Mar 3;281(9):5973-81. Epub 2005 Dec 21. PMID:16373351<ref>PMID:16373351</ref>
-BDM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with HEM, TMI and CM5 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Unspecific_monooxygenase Unspecific monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.1 1.14.14.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BDM OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction., Zhao Y, White MA, Muralidhara BK, Sun L, Halpert JR, Stout CD, J Biol Chem. 2006 Mar 3;281(9):5973-81. Epub 2005 Dec 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16373351 16373351]
+</div>
+<div class="pdbe-citations 2bdm" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: Single protein]]
+[[Category: Halpert JR]]
-[[Category: Unspecific monooxygenase]]
+[[Category: Muralidhara BK]]
-[[Category: Halpert, J.R.]]
+[[Category: Stout CD]]
-[[Category: Muralidhara, B.K.]]
+[[Category: Sun L]]
-[[Category: Stout, C.D.]]
+[[Category: White MA]]
-[[Category: Sun, L.]]
+[[Category: Zhao Y]]
-[[Category: White, M.A.]]
-[[Category: Zhao, Y.]]
-[[Category: CM5]]
-[[Category: HEM]]
-[[Category: TMI]]
-[[Category: cyp 2b4]]
-[[Category: cyp lm2]]
-[[Category: membrane protein]]
-[[Category: monooxygenase]]
-[[Category: oxidoreductase]]
-[[Category: p450]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:44:50 2007''