3dbm: 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:3dbm.png|left|200px]]
-{{STRUCTURE_3dbm|  PDB=3dbm  |  SCENE=  }}
+==Crystal Structure of Allene oxide synthase==
+<StructureSection load='3dbm' size='340' side='right'caption='[[3dbm]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3dbm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Parthenium_argentatum Parthenium argentatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DBM 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]] 2.6&#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=HO2:(9E,11E,13S)-13-HYDROXYOCTADECA-9,11-DIENOIC+ACID'>HO2</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=3dbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbm OCA], [https://pdbe.org/3dbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dbm RCSB], [https://www.ebi.ac.uk/pdbsum/3dbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dbm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/C74A2_PARAR C74A2_PARAR] Involved in the biosynthesis of jasmonic acid, a growth regulator that is implicated also as a signaling molecule in plant defense. Acts on a number of unsaturated fatty-acid hydroperoxides, forming the corresponding allene oxides (By similarity).
+== 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/db/3dbm_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=3dbm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cytochrome P450s exist ubiquitously in all organisms and are involved in many biological processes. Allene oxide synthase (AOS) is a P450 enzyme that plays a key role in the biosynthesis of oxylipin jasmonates, which are involved in signal and defense reactions in higher plants. The crystal structures of guayule (Parthenium argentatum) AOS (CYP74A2) and its complex with the substrate analog 13(S)-hydroxyoctadeca-9Z,11E-dienoic acid have been determined. The structures exhibit a classic P450 fold but possess a heme-binding mode with an unusually long heme binding loop and a unique I-helix. The structures also reveal two channels through which substrate and product may access and leave the active site. The entrances are defined by a loop between beta3-2 and beta3-3. Asn-276 in the substrate binding site may interact with the substrate's hydroperoxy group and play an important role in catalysis, and Lys-282 at the entrance may control substrate access and binding. These studies provide both structural insights into AOS and related P450s and a structural basis to understand the distinct reaction mechanism.
-===Crystal Structure of Allene oxide synthase===
+Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase.,Li L, Chang Z, Pan Z, Fu ZQ, Wang X Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13883-8. Epub 2008 Sep 11. PMID:18787124<ref>PMID:18787124</ref>
-{{ABSTRACT_PUBMED_18787124}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3dbm" style="background-color:#fffaf0;"></div>
-[[3dbm]] is a 1 chain structure of [[Cytochrome P450]] with sequence from [http://en.wikipedia.org/wiki/Parthenium_argentatum Parthenium argentatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBM OCA].
 ==See Also==
-*[[Cytochrome P450|Cytochrome P450]]
+*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018787124</ref><references group="xtra"/>
+__TOC__
-[[Category: Hydroperoxide dehydratase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Parthenium argentatum]]
-[[Category: Li, L.]]
+[[Category: Li L]]
-[[Category: Wang, X.]]
+[[Category: Wang X]]
-[[Category: Crystal structure hem hode ao]]
-[[Category: Fatty acid biosynthesis]]
-[[Category: Heme]]
-[[Category: Iron]]
-[[Category: Lipid synthesis]]
-[[Category: Lyase]]
-[[Category: Metal-binding]]
-[[Category: Oxylipin biosynthesis]]