3lc4: Difference between revisions

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-[[Image:3lc4.png|left|200px]]
-<!--
+==Human Cytochrome P450 2E1 in Complex with Omega-Imidazolyl-Dodecanoic Acid==
-The line below this paragraph, containing "STRUCTURE_3lc4", creates the "Structure Box" on the page.
+<StructureSection load='3lc4' size='340' side='right'caption='[[3lc4]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3lc4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LC4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LC4:12-(1H-IMIDAZOL-1-YL)DODECANOIC+ACID'>LC4</scene></td></tr>
-{{STRUCTURE_3lc4|  PDB=3lc4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3lc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lc4 OCA], [https://pdbe.org/3lc4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lc4 RCSB], [https://www.ebi.ac.uk/pdbsum/3lc4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lc4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CP2E1_HUMAN CP2E1_HUMAN] Metabolizes several precarcinogens, drugs, and solvents to reactive metabolites. Inactivates a number of drugs and xenobiotics and also bioactivates many xenobiotic substrates to their hepatotoxic or carcinogenic forms.
+== 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/lc/3lc4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3lc4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human microsomal cytochrome P450 (CYP) 2E1 is widely known for its ability to oxidize &gt;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.
-===Human Cytochrome P450 2E1 in Complex with Omega-Imidazolyl-Dodecanoic Acid===
+Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode.,Porubsky PR, Battaile KP, Scott EE J Biol Chem. 2010 Jul 16;285(29):22282-90. Epub 2010 May 12. PMID:20463018<ref>PMID:20463018</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_20463018}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3lc4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20463018 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_20463018}}
-==About this Structure==
-[[3lc4]] is a 2 chain structure of [[Cytochrome P450]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LC4 OCA].
 ==See Also==
-*[[Cytochrome P450]]
+*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:20463018</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Porubsky, P R.]]
+[[Category: Large Structures]]
-[[Category: Scott, E E.]]
+[[Category: Porubsky PR]]
-[[Category: Acetaminophen]]
+[[Category: Scott EE]]
-[[Category: Cyp2e1]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Heme]]
-[[Category: Iron]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Microsome]]
-[[Category: Monooxygenase]]
-[[Category: Oxidoreductase]]
-[[Category: P450 2e1]]