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| [[Image:1wlu.gif|left|200px]]<br /><applet load="1wlu" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="1wlu, resolution 1.45Å" />
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| '''Crystal structure of TT0310 protein from Thermus thermophilus HB8'''<br />
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| ==Overview== | | ==Crystal structure of TT0310 protein from Thermus thermophilus HB8== |
| Hot dog fold proteins sharing the characteristic "hot dog" fold are known to involve certain coenzyme A binding enzymes with various oligomeric states. In order to elucidate the oligomerization-function relationship of the hot dog fold proteins, crystal structures of the phenylacetate degradation protein PaaI from Thermus thermophilus HB8 (TtPaaI), a tetrameric acyl-CoA thioesterase with the hot dog fold, have been determined and compared with those of other family members. In the liganded crystal forms with coenzyme A derivatives, only two of four intersubunit catalytic pockets of the TtPaaI tetramer are occupied by the ligands. A detailed structural comparison between several liganded and unliganded forms reveals that a subtle rigid-body rearrangement of subunits within 2 degrees upon binding of the first two ligand molecules can induce a strict negative cooperativity to prevent further binding at the remaining two pockets, indicating that the so-called "half-of-the-sites reactivity" of oligomeric enzymes is visualized for the first time. Considering kinetic and mutational analyses together, a possible reaction mechanism of TtPaaI is proposed; one tetramer binds only two acyl-CoA molecules with a novel asymmetric induced-fit mechanism and carries out the hydrolysis according to a base-catalyzed reaction through activation of a water molecule by Asp48. From a structural comparison with other family members, it is concluded that a subgroup of the hot dog fold protein family, referred to as "asymmetric hot dog thioesterases" including medium chain acyl-CoA thioesterase II from Escherichia coli and human thioesterase III, might share the same oligomerization mode and the asymmetric induced-fit mechanism as observed in TtPaaI.
| | <StructureSection load='1wlu' size='340' side='right'caption='[[1wlu]], [[Resolution|resolution]] 1.45Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1wlu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WLU FirstGlance]. <br> |
| 1WLU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WLU 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]] 1.45Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=1wlu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wlu OCA], [https://pdbe.org/1wlu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wlu RCSB], [https://www.ebi.ac.uk/pdbsum/1wlu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wlu ProSAT], [https://www.topsan.org/Proteins/RSGI/1wlu TOPSAN]</span></td></tr> |
| A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI., Kunishima N, Asada Y, Sugahara M, Ishijima J, Nodake Y, Sugahara M, Miyano M, Kuramitsu S, Yokoyama S, Sugahara M, J Mol Biol. 2005 Sep 9;352(1):212-28. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16061252 16061252]
| | </table> |
| [[Category: Single protein]] | | == Function == |
| [[Category: Thermus thermophilus]] | | [https://www.uniprot.org/uniprot/Q5SJP3_THET8 Q5SJP3_THET8] |
| [[Category: Kunishima, N.]] | | == Evolutionary Conservation == |
| [[Category: Miyano, M.]]
| | [[Image:Consurf_key_small.gif|200px|right]] |
| [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
| | Check<jmol> |
| [[Category: Sugahara, M.]] | | <jmolCheckbox> |
| [[Category: CL]] | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wl/1wlu_consurf.spt"</scriptWhenChecked> |
| [[Category: GOL]] | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| [[Category: hot dog fold]]
| | <text>to colour the structure by Evolutionary Conservation</text> |
| [[Category: phenylacetic acid degradation]] | | </jmolCheckbox> |
| [[Category: riken structural genomics/proteomics initiative]] | | </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=1wlu ConSurf]. |
| [[Category: rsgi]] | | <div style="clear:both"></div> |
| [[Category: structural genomics]] | | __TOC__ |
| [[Category: thioesterase]] | | </StructureSection> |
| | | [[Category: Large Structures]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:45:43 2008''
| | [[Category: Thermus thermophilus HB8]] |
| | [[Category: Kunishima N]] |
| | [[Category: Miyano M]] |
| | [[Category: Sugahara M]] |
