2ix5: Difference between revisions
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<StructureSection load='2ix5' size='340' side='right' caption='[[2ix5]], [[Resolution|resolution]] 2.70Å' scene=''> | ==Short chain specific acyl-CoA oxidase from Arabidopsis thaliana, ACX4 in complex with acetoacetyl-CoA== | ||
<StructureSection load='2ix5' size='340' side='right'caption='[[2ix5]], [[Resolution|resolution]] 2.70Å' scene=''> | |||
== Structural highlights == | == Structural highlights == | ||
[[2ix5]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2ix5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IX5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IX5 FirstGlance]. <br> | ||
<b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>< | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=2ix5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ix5 OCA], [https://pdbe.org/2ix5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ix5 RCSB], [https://www.ebi.ac.uk/pdbsum/2ix5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ix5 ProSAT]</span></td></tr> | ||
<b>Resources:</b> <span class='plainlinks'>[ | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/ACOX4_ARATH ACOX4_ARATH] Catalyzes the desaturation of short-chain acyl-CoAs to 2-trans-enoyl-CoAs. Active on butyryl-CoA (C4), hexanoyl-CoA (C6), and octanoyl-CoA (C8). Has no activity as acyl-CoA dehydrogenase or on crotonyl-CoA (an unsaturated C4:1 carbocyclic ester) or glutaryl-CoA (a dicarboxylic ester). | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/2ix5_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/2ix5_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2ix5 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
Plants produce a unique peroxisomal short chain-specific acyl-CoA oxidase (ACX4) for beta-oxidation of lipids. The short chain-specific oxidase has little resemblance to other peroxisomal acyl-CoA oxidases but has an approximately 30% sequence identity to mitochondrial acyl-CoA dehydrogenases. Two biochemical features have been linked to structural properties by comparing the structures of short chain-specific Arabidopsis thaliana ACX4 with and without a substrate analogue bound in the active site to known acyl-CoA oxidases and dehydrogenase structures: (i) a solvent-accessible acyl binding pocket is not required for oxygen reactivity, and (ii) the oligomeric state plays a role in substrate pocket architecture but is not linked to oxygen reactivity. The structures indicate that the acyl-CoA oxidases may encapsulate the electrons for transfer to molecular oxygen by blocking the dehydrogenase substrate interaction site with structural extensions. A small binding pocket observed adjoining the flavin adenine dinucleotide N5 and C4a atoms could increase the number of productive encounters between flavin adenine dinucleotide and O2. | Plants produce a unique peroxisomal short chain-specific acyl-CoA oxidase (ACX4) for beta-oxidation of lipids. The short chain-specific oxidase has little resemblance to other peroxisomal acyl-CoA oxidases but has an approximately 30% sequence identity to mitochondrial acyl-CoA dehydrogenases. Two biochemical features have been linked to structural properties by comparing the structures of short chain-specific Arabidopsis thaliana ACX4 with and without a substrate analogue bound in the active site to known acyl-CoA oxidases and dehydrogenase structures: (i) a solvent-accessible acyl binding pocket is not required for oxygen reactivity, and (ii) the oligomeric state plays a role in substrate pocket architecture but is not linked to oxygen reactivity. The structures indicate that the acyl-CoA oxidases may encapsulate the electrons for transfer to molecular oxygen by blocking the dehydrogenase substrate interaction site with structural extensions. A small binding pocket observed adjoining the flavin adenine dinucleotide N5 and C4a atoms could increase the number of productive encounters between flavin adenine dinucleotide and O2. | ||
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Controlling electron transfer in Acyl-CoA oxidases and dehydrogenases: a structural view.,Mackenzie J, Pedersen L, Arent S, Henriksen A J Biol Chem. 2006 Oct 13;281(41):31012-20. Epub 2006 Aug 3. PMID:16887802<ref>PMID:16887802</ref> | Controlling electron transfer in Acyl-CoA oxidases and dehydrogenases: a structural view.,Mackenzie J, Pedersen L, Arent S, Henriksen A J Biol Chem. 2006 Oct 13;281(41):31012-20. Epub 2006 Aug 3. PMID:16887802<ref>PMID:16887802</ref> | ||
From | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
<div class="pdbe-citations 2ix5" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Arabidopsis thaliana]] | [[Category: Arabidopsis thaliana]] | ||
[[Category: Arent | [[Category: Large Structures]] | ||
[[Category: Henriksen | [[Category: Arent S]] | ||
[[Category: Mackenzie | [[Category: Henriksen A]] | ||
[[Category: Pedersen | [[Category: Mackenzie J]] | ||
[[Category: Pedersen L]] | |||