3e5k: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3e5k.png|left|200px]]
-<!--
+==Crystal structure of CYP105P1 wild-type 4-phenylimidazole complex==
-The line below this paragraph, containing "STRUCTURE_3e5k", creates the "Structure Box" on the page.
+<StructureSection load='3e5k' size='340' side='right'caption='[[3e5k]], [[Resolution|resolution]] 2.60&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'>[[3e5k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E5K 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]] 2.6&#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=PIM:4-PHENYL-1H-IMIDAZOLE'>PIM</scene></td></tr>
-{{STRUCTURE_3e5k|  PDB=3e5k  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3e5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e5k OCA], [https://pdbe.org/3e5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e5k RCSB], [https://www.ebi.ac.uk/pdbsum/3e5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e5k ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q93H81_STRAX Q93H81_STRAX]
+== 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/e5/3e5k_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=3e5k ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The polyene macrolide antibiotic filipin is widely used as a probe for cholesterol in biological membranes. The filipin biosynthetic pathway of Streptomyces avermitilis contains two position-specific hydroxylases, C26-specific CYP105P1 and C1'-specific CYP105D6. In this study, we describe the three X-ray crystal structures of CYP105P1: the ligand-free wild-type (WT-free), 4-phenylimidazole-bound wild-type (WT-4PI), and ligand-free H72A mutant (H72A-free) forms. The BC loop region in the WT-free structure has a unique feature; the side chain of His72 within this region is ligated to the heme iron. On the other hand, this region is highly disordered and widely open in WT-4PI and H72A-free structures, respectively. Histidine ligation of wild-type CYP105P1 was not detectable in solution, and a type II spectral change was clearly observed when 4-phenylimidazole was titrated. The H72A mutant showed spectroscopic characteristics that were almost identical to those of the wild-type protein. In the H72A-free structure, there is a large pocket that is of the same size as the filipin molecule. The highly flexible feature of the BC loop region of CYP105P1 may be required to accept a large hydrophobic substrate.
-===Crystal structure of CYP105P1 wild-type 4-phenylimidazole complex===
+Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis: conformational flexibility and histidine ligation state.,Xu LH, Fushinobu S, Ikeda H, Wakagi T, Shoun H J Bacteriol. 2009 Feb;191(4):1211-9. Epub 2008 Dec 12. PMID:19074393<ref>PMID:19074393</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_19074393}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3e5k" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19074393 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_19074393}}
-==About this Structure==
-[[3e5k]] is a 1 chain structure of [[Cytochrome P450]] with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E5K OCA].
 ==See Also==
-*[[Cytochrome P450]]
+*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
+*[[Cytochrome P450 hydroxylase 3D structures|Cytochrome P450 hydroxylase 3D structures]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:19074393</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces avermitilis]]
-[[Category: Fushinobu, S.]]
+[[Category: Fushinobu S]]
-[[Category: Ikeda, H.]]
+[[Category: Ikeda H]]
-[[Category: Shoun, H.]]
+[[Category: Shoun H]]
-[[Category: Wakagi, T.]]
+[[Category: Wakagi T]]
-[[Category: Xu, L H.]]
+[[Category: Xu LH]]
-[[Category: Heme]]
-[[Category: Iron]]
-[[Category: Metal-binding]]
-[[Category: Monooxygenase]]
-[[Category: Oxidoreductase]]
-[[Category: P450]]