|
|
| (12 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:1wm6.gif|left|200px]] | |
| | | | |
| - | {{Structure
| + | ==Crystal structure of TT0310 protein from Thermus thermophilus HB8== |
| - | |PDB= 1wm6 |SIZE=350|CAPTION= <scene name='initialview01'>1wm6</scene>, resolution 2.40Å
| + | <StructureSection load='1wm6' size='340' side='right'caption='[[1wm6]], [[Resolution|resolution]] 2.40Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> | + | <table><tr><td colspan='2'>[[1wm6]] is a 8 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=1WM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WM6 FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wm6 OCA], [https://pdbe.org/1wm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wm6 RCSB], [https://www.ebi.ac.uk/pdbsum/1wm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wm6 ProSAT], [https://www.topsan.org/Proteins/RSGI/1wm6 TOPSAN]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wm6 OCA], [http://www.ebi.ac.uk/pdbsum/1wm6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wm6 RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/Q5SJP3_THET8 Q5SJP3_THET8] |
| - | | + | == Evolutionary Conservation == |
| - | '''Crystal structure of TT0310 protein from Thermus thermophilus HB8'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wm/1wm6_consurf.spt"</scriptWhenChecked> |
| - | 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.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1WM6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WM6 OCA].
| + | </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=1wm6 ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference== | + | __TOC__ |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/16061252 16061252]
| + | </StructureSection> |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Thermus thermophilus]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Kunishima, N.]] | + | [[Category: Kunishima N]] |
| - | [[Category: Miyano, M.]] | + | [[Category: Miyano M]] |
| - | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
| + | [[Category: Sugahara M]] |
| - | [[Category: Sugahara, M.]] | + | |
| - | [[Category: hot dog fold]]
| + | |
| - | [[Category: phenylacetic acid degradation]]
| + | |
| - | [[Category: riken structural genomics/proteomics initiative]]
| + | |
| - | [[Category: rsgi]]
| + | |
| - | [[Category: structural genomic]]
| + | |
| - | [[Category: thioesterase]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:38:07 2008''
| + | |
