1yge

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[[Image:1yge.jpg|left|200px]]
 
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==LIPOXYGENASE-1 (SOYBEAN) AT 100K==
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The line below this paragraph, containing "STRUCTURE_1yge", creates the "Structure Box" on the page.
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<StructureSection load='1yge' size='340' side='right'caption='[[1yge]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1yge]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YGE FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
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{{STRUCTURE_1yge| PDB=1yge | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yge OCA], [https://pdbe.org/1yge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yge RCSB], [https://www.ebi.ac.uk/pdbsum/1yge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yge ProSAT]</span></td></tr>
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</table>
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'''LIPOXYGENASE-1 (SOYBEAN) AT 100K'''
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== Function ==
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[https://www.uniprot.org/uniprot/LOX1_SOYBN LOX1_SOYBN] Plant lipoxygenase may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. With linoleate as substrate, L-1 shows a preference for carbon 13 as the site for hydroperoxidation (in contrast to L-2 and L-3, which utilize either carbon 9 or 13). At pH above 8.5, only (9Z,11E,13S)-13-hydroperoxyoctadeca-9,11-dienoate is produced, but as the pH decreases, the proportion of (9S)-hydroperoxide increases linearly until at pH 6.0 it represents about 25 % of the products.<ref>PMID:16157595</ref>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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Lipoxygenases, which are widely distributed among plant and animal species, are Fe-containing dioxygenases that act on lipids containing (Z,Z)-pentadiene moieties in the synthesis of compounds with a variety of functions. Utilizing an improved strategy of data collection, low temperature, and synchrotron radiation of short wavelength, the structure of ferrous soybean lipoxygenase L-1, a single chain protein of 839 amino acid residues, has been determined by X-ray crystallography to a resolution of 1.4 A. The R-factor for the refined model is 19.7%. General features of the protein structure were found to be consistent with the results of prior crystallographic studies at lower (2.6 A) resolution. In contrast to the prior studies, the binding of a water molecule to the active site Fe was established. The octahedral coordination sphere of the Fe also includes the side chains of His499, His504, His690, and Asn694 as well as the terminal carboxylate of Ile839, which binds as a monodentate ligand. Asn694 is involved in a number of labile polar interactions with other protein groups, including an amide-aromatic hydrogen bond, and appears to be a weak ligand. Several possible access routes for dioxygen and fatty acids to the internal active site and substrate binding cavity are described. The protein structure restricts access to the Fe site such that the formation of an organo-Fe intermediate seems improbable. Structural restrictions pertinent to other proposed reaction intermediates, such as planar pentadienyl and nonplanar allyl radicals, are also discussed.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yg/1yge_consurf.spt"</scriptWhenChecked>
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1YGE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YGE OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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Crystal structure of soybean lipoxygenase L-1 at 1.4 A resolution., Minor W, Steczko J, Stec B, Otwinowski Z, Bolin JT, Walter R, Axelrod B, Biochemistry. 1996 Aug 20;35(33):10687-701. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8718858 8718858]
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</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=1yge ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Glycine max]]
[[Category: Glycine max]]
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[[Category: Lipoxygenase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Axelrod B]]
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[[Category: Axelrod, B.]]
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[[Category: Bolin JT]]
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[[Category: Bolin, J T.]]
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[[Category: Minor W]]
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[[Category: Minor, W.]]
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[[Category: Otwinowski Z]]
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[[Category: Otwinowski, Z.]]
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[[Category: Stec B]]
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[[Category: Stec, B.]]
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[[Category: Steczko J]]
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[[Category: Steczko, J.]]
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[[Category: Walter R]]
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[[Category: Walter, R.]]
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[[Category: Dioxygenase]]
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[[Category: Fatty acid]]
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[[Category: Lipoxygenase]]
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[[Category: Metalloprotein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 16:17:13 2008''
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Current revision

LIPOXYGENASE-1 (SOYBEAN) AT 100K

PDB ID 1yge

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