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| [[Image:1oqb.gif|left|200px]]<br /><applet load="1oqb" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="1oqb, resolution 2.80Å" />
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| '''The Crystal Structure of the one-iron form of the di-iron center in Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean).'''<br />
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| ==Overview== | | ==The Crystal Structure of the one-iron form of the di-iron center in Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean).== |
| Delta9 stearoyl-acyl carrier protein (ACP) desaturase is a mu-oxo-bridged di-iron enzyme, which belongs to the structural class I of large helix bundle proteins and that catalyzes the NADPH and O2-dependent formation of a cis-double bond in stearoyl-ACP. The crystal structures of complexes with azide and acetate, respectively, as well as the apoand single-iron forms of Delta9 stearoyl-ACP desaturase from Ricinus communis have been determined. In the azide complex, the ligand forms a mu-1,3-bridge between the two iron ions in the active site, replacing a loosely bound water molecule. The structure of the acetate complex is similar, with acetate bridging the di-iron center in the same orientation with respect to the di-iron center. However, in this complex, the iron ligand Glu196 has changed its coordination mode from bidentate to monodentate, the first crystallographic observation of a carboxylate shift in Delta9 stearoyl-ACP desaturase. The two complexes are proposed to mimic a mu-1,2 peroxo intermediate present during catalytic turnover. There are striking structural similarities between the di-iron center in the Delta9 stearoyl-ACP desaturase-azide complex and in the reduced rubrerythrin-azide complex. This suggests that Delta9 stearoyl-ACP desaturase might catalyze the formation of water from exogenous hydrogen peroxide at a low rate. From the similarity in iron center structure, we propose that the mu-oxo-bridge in oxidized desaturase is bound to the di-iron center as in rubrerythrin and not as reported for the R2 subunit of ribonucleotide reductase and the hydroxylase subunit of methane monooxygenase. The crystal structure of the one-iron depleted desaturase species demonstrates that the affinities for the two iron ions comprising the di-iron center are not equivalent, Fe1 being the higher affinity site and Fe2 being the lower affinity site.
| | <StructureSection load='1oqb' size='340' side='right'caption='[[1oqb]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1oqb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OQB FirstGlance]. <br> |
| 1OQB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis] with <scene name='pdbligand=FE2:'>FE2</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Acyl-[acyl-carrier-protein]_desaturase Acyl-[acyl-carrier-protein] desaturase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.19.2 1.14.19.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQB OCA].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr> |
| ==Reference== | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqb OCA], [https://pdbe.org/1oqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oqb RCSB], [https://www.ebi.ac.uk/pdbsum/1oqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqb ProSAT]</span></td></tr> |
| Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates., Moche M, Shanklin J, Ghoshal A, Lindqvist Y, J Biol Chem. 2003 Jul 4;278(27):25072-80. Epub 2003 Apr 18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12704186 12704186]
| | </table> |
| [[Category: Acyl-[acyl-carrier-protein] desaturase]] | | == Function == |
| | [https://www.uniprot.org/uniprot/STAD_RICCO STAD_RICCO] Converts stearoyl-ACP to oleoyl-ACP by introduction of a cis double bond between carbons Delta(9) and Delta(10) of the acyl chain. |
| | == 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/oq/1oqb_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=1oqb ConSurf]. |
| | <div style="clear:both"></div> |
| | __TOC__ |
| | </StructureSection> |
| | [[Category: Large Structures]] |
| [[Category: Ricinus communis]] | | [[Category: Ricinus communis]] |
| [[Category: Single protein]]
| | [[Category: Ghoshal AK]] |
| [[Category: Ghoshal, A K.]] | | [[Category: Lindqvist Y]] |
| [[Category: Lindqvist, Y.]] | | [[Category: Moche M]] |
| [[Category: Moche, M.]] | | [[Category: Shanklin J]] |
| [[Category: Shanklin, J.]] | |
| [[Category: FE2]]
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| [[Category: di-iron enzyme]]
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| [[Category: electron transfer]]
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| [[Category: fatty acid biosynthesis]]
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| [[Category: four-helix bundle]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:20:24 2008''
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