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New page: left|200px<br /><applet load="1wlu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wlu, resolution 1.45Å" /> '''Crystal structure of...
 
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[[Image:1wlu.gif|left|200px]]<br /><applet load="1wlu" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1wlu, resolution 1.45&Aring;" />
'''Crystal structure of TT0310 protein from Thermus thermophilus HB8'''<br />


==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]] 1.45&Aring;' 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 CL and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.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]] 1.45&#8491;</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://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:12:27 2007''
[[Category: Thermus thermophilus HB8]]
[[Category: Kunishima N]]
[[Category: Miyano M]]
[[Category: Sugahara M]]
Retrieved from "https://proteopedia.org/1wlu"