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| - | [[Image:1euz.jpg|left|200px]]<br /><applet load="1euz" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1euz, resolution 2.25Å" /> | |
| - | '''GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGATED STATE'''<br /> | |
| | | | |
| - | ==Overview== | + | ==GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGATED STATE== |
| - | Here we describe the large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase. Glutamate dehydrogenase from Thermococcus profundus is composed of six identical subunits of M(r) 46K, each with two distinct domains of roughly equal size separated by a large active-site cleft. The enzyme in the unligated state was crystallized so that one hexamer occupied a crystallographic asymmetric unit, and the crystal structure of the hexamer was solved and refined at a resolution of 2.25 A with a crystallographic R-factor of 0.190. In that structure, the six subunits displayed significant conformational variations with respect to the orientations of the two domains. The variation was most likely explained as a hinge-bending motion caused by small changes in the main chain torsion angle of the residue composing a loop connecting the two domains. Small-angle X-ray scattering profiles both at 293 and 338 K suggested that the apparent molecular size of the hexamer was slightly larger in solution than in the crystalline state. These results led us to the conclusion that (i) the spontaneous domain motion was the property of the enzyme in solution, (ii) the domain motion was trapped in the crystallization process through different modes of crystal contacts, and (iii) the magnitude of the motion in solution was greater than that observed in the crystal structure. The present cryogenic diffraction experiment enabled us to identify 1931 hydration water molecules around the hexamer. The hydration structures around the subunits exhibited significant changes in accord with the degree of the domain movement. In particular, the hydration water molecules in the active-site cleft were rearranged markedly through migrations between specific hydration sites in coupling strongly with the domain movement. We discussed the cooperative dynamics between the domain motion and the hydration structure changes in the active site of the enzyme. The present study provides the first example of a visualized hydration structure varying transiently with the dynamic movements of enzymes and may form a new concept of the dynamics of multidomain enzymes in solution.
| + | <StructureSection load='1euz' size='340' side='right'caption='[[1euz]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1euz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_profundus Thermococcus profundus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EUZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EUZ 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]] 2.25Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1euz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1euz OCA], [https://pdbe.org/1euz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1euz RCSB], [https://www.ebi.ac.uk/pdbsum/1euz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1euz ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DHE3_THEPR DHE3_THEPR] |
| | + | == 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/eu/1euz_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=1euz ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | ==About this Structure== | + | ==See Also== |
| - | 1EUZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_profundus Thermococcus profundus] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glutamate_dehydrogenase Glutamate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.2 1.4.1.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EUZ OCA].
| + | *[[Glutamate dehydrogenase 3D structures|Glutamate dehydrogenase 3D structures]] |
| - | | + | __TOC__ |
| - | ==Reference==
| + | </StructureSection> |
| - | Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering., Nakasako M, Fujisawa T, Adachi S, Kudo T, Higuchi S, Biochemistry. 2001 Mar 13;40(10):3069-79. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11258921 11258921]
| + | [[Category: Large Structures]] |
| - | [[Category: Glutamate dehydrogenase]] | + | |
| - | [[Category: Single protein]]
| + | |
| | [[Category: Thermococcus profundus]] | | [[Category: Thermococcus profundus]] |
| - | [[Category: Nakasako, M.]] | + | [[Category: Nakasako M]] |
| - | [[Category: SO4]]
| + | |
| - | [[Category: domain closure movement]]
| + | |
| - | [[Category: glutamate]]
| + | |
| - | [[Category: hyperthermostability]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:31:46 2008''
| + | |
