|
|
| (19 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| [[Image:1amj.gif|left|200px]]<br /><applet load="1amj" size="350" color="white" frame="true" align="right" spinBox="true"
| |
| caption="1amj, resolution 2.0Å" />
| |
| '''STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM'''<br />
| |
|
| |
|
| ==Overview== | | ==STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM== |
| Crystal structures of mitochondrial aconitase with alpha-methylisocitrate and with sulfate bound have been solved and refined at 2.0 A resolution with R factors of 18.2 and 16.8%, respectively. The steric factors and conformational effects observed in both new structures support the proposed mechanism for the overall reaction catalyzed by aconitase. The alternate substrate alpha-methylisocitrate is derived from alpha-methyl-cis-aconitate during crystallization and is observed to bind in the active site in a manner very similar to that observed for isocitrate. The methyl group is accommodated by favorable contact with Ile-425. However, the other potential hydration product of alpha-methyl-cis-aconitate, alpha-methylcitrate, cannot be accommodated in the active site due to steric conflict of the methyl group with Asp-165. The results are consistent with the requirement that cis-aconitate must bind in two ways, in the citrate mode and in the isocitrate mode. Crystals of aconitase with sulfate bound are isomorphous to those with isocitrate bound. However, the structure displays significant conformational changes, providing a model for the substrate-free state of enzyme. Three water molecules bind in place of the C alpha- and C beta-hydroxyl and carboxyl groups of isocitrate, while sulfate binds in place of the C gamma-carboxyl group. Side chains of Ser-642 and Arg-447 in the active site rotate to pair with other side chains in the absence of substrate. The new conformation of Arg-447 triggers a concerted set of shifts which transmits conformational change to the surface of the protein, 30 A from the active site. In the absence of substrate, a chain segment containing the [4Fe-4S] ligand Cys-358 also shifts, resulting in the net translation and reorientation of the Fe-S cluster.
| | <StructureSection load='1amj' size='340' side='right'caption='[[1amj]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == |
| | <table><tr><td colspan='2'>[[1amj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AMJ 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]] 2Å</td></tr> |
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1amj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1amj OCA], [https://pdbe.org/1amj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1amj RCSB], [https://www.ebi.ac.uk/pdbsum/1amj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1amj ProSAT]</span></td></tr> |
| | </table> |
| | == Function == |
| | [https://www.uniprot.org/uniprot/ACON_BOVIN ACON_BOVIN] Catalyzes the isomerization of citrate to isocitrate via cis-aconitate. |
| | == 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/am/1amj_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=1amj ConSurf]. |
| | <div style="clear:both"></div> |
|
| |
|
| ==About this Structure== | | ==See Also== |
| 1AMJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with <scene name='pdbligand=OH:'>OH</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=SF4:'>SF4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aconitate_hydratase Aconitate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.3 4.2.1.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AMJ OCA].
| | *[[Aconitase|Aconitase]] |
| | | *[[Aconitase 3D structures|Aconitase 3D structures]] |
| ==Reference==
| | __TOC__ |
| Steric and conformational features of the aconitase mechanism., Lauble H, Stout CD, Proteins. 1995 May;22(1):1-11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7675781 7675781]
| | </StructureSection> |
| [[Category: Aconitate hydratase]]
| |
| [[Category: Bos taurus]] | | [[Category: Bos taurus]] |
| [[Category: Single protein]] | | [[Category: Large Structures]] |
| [[Category: Stout, C D.]] | | [[Category: Stout CD]] |
| [[Category: OH]]
| |
| [[Category: SF4]]
| |
| [[Category: SO4]]
| |
| [[Category: lyase(carbon-oxygen)]]
| |
| | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:46:05 2008''
| |