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2v3t

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[[Image:2v3t.gif|left|200px]]<br />
 
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<applet load="2v3t" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2v3t, resolution 2.75&Aring;" />
 
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'''STRUCTURE OF THE LIGAND-BINDING CORE OF THE IONOTROPIC GLUTAMATE RECEPTOR-LIKE GLURDELTA2 IN THE APO FORM'''<br />
 
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==Overview==
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==Structure of the ligand-binding core of the ionotropic glutamate receptor-like GluRdelta2 in the apo form==
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The orphan glutamate-like receptor GluRdelta2 is predominantly expressed, in Purkinje cells of the central nervous system. The classification of, GluRdelta2 to the ionotropic glutamate receptor family is based on, sequence similarities, because GluRdelta2 does not form functional, homomeric glutamate-gated ion channels in transfected cells. Studies in, GluRdelta2(-/-) knockout mice as well as in mice with naturally occurring, mutations in the GluRdelta2 gene have demonstrated an essential role of, GluRdelta2 in cerebellar long-term depression, motor learning, motor, coordination, and synaptogenesis. However, the lack of a known agonist has, hampered investigations on the function of GluRdelta2. In this study, the, ligand-binding core of GluRdelta2 (GluRdelta2-S1S2) was found to bind, neutral amino acids such as d-serine and glycine, as demonstrated by, isothermal titration calorimetry. Direct evidence for binding of d-serine, and structural rearrangements in the binding cleft of GluRdelta2-S1S2 is, provided by x-ray structures of GluRdelta2-S1S2 in its apo form and in, complex with d-serine. Functionally, d-serine and glycine were shown to, inactivate spontaneous ion-channel conductance in GluRdelta2 containing, the lurcher mutation (EC(50) values, 182 and 507 muM, respectively). These, data demonstrate that the GluRdelta2 ligand-binding core is capable of, binding ligands and that cleft closure of the ligand-binding core can, induce conformational changes that alter ion permeation.
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<StructureSection load='2v3t' size='340' side='right'caption='[[2v3t]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2v3t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V3T FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2v3u|2v3u]]</div></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v3t OCA], [https://pdbe.org/2v3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v3t RCSB], [https://www.ebi.ac.uk/pdbsum/2v3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v3t ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v3/2v3t_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2v3t ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The orphan glutamate-like receptor GluRdelta2 is predominantly expressed in Purkinje cells of the central nervous system. The classification of GluRdelta2 to the ionotropic glutamate receptor family is based on sequence similarities, because GluRdelta2 does not form functional homomeric glutamate-gated ion channels in transfected cells. Studies in GluRdelta2(-/-) knockout mice as well as in mice with naturally occurring mutations in the GluRdelta2 gene have demonstrated an essential role of GluRdelta2 in cerebellar long-term depression, motor learning, motor coordination, and synaptogenesis. However, the lack of a known agonist has hampered investigations on the function of GluRdelta2. In this study, the ligand-binding core of GluRdelta2 (GluRdelta2-S1S2) was found to bind neutral amino acids such as D-serine and glycine, as demonstrated by isothermal titration calorimetry. Direct evidence for binding of D-serine and structural rearrangements in the binding cleft of GluRdelta2-S1S2 is provided by x-ray structures of GluRdelta2-S1S2 in its apo form and in complex with D-serine. Functionally, D-serine and glycine were shown to inactivate spontaneous ion-channel conductance in GluRdelta2 containing the lurcher mutation (EC(50) values, 182 and 507 microM, respectively). These data demonstrate that the GluRdelta2 ligand-binding core is capable of binding ligands and that cleft closure of the ligand-binding core can induce conformational changes that alter ion permeation.
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==About this Structure==
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Ionotropic glutamate-like receptor delta2 binds D-serine and glycine.,Naur P, Hansen KB, Kristensen AS, Dravid SM, Pickering DS, Olsen L, Vestergaard B, Egebjerg J, Gajhede M, Traynelis SF, Kastrup JS Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):14116-21. Epub 2007 Aug 21. PMID:17715062<ref>PMID:17715062</ref>
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2V3T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2V3T OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Ionotropic glutamate-like receptor {delta}2 binds D-serine and glycine., Naur P, Hansen KB, Kristensen AS, Dravid SM, Pickering DS, Olsen L, Vestergaard B, Egebjerg J, Gajhede M, Traynelis SF, Kastrup JS, Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):14116-21. Epub 2007 Aug 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17715062 17715062]
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</div>
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[[Category: Rattus norvegicus]]
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<div class="pdbe-citations 2v3t" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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== References ==
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[[Category: Gajhede, M.]]
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<references/>
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[[Category: Kastrup, J.S.]]
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__TOC__
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[[Category: Naur, P.]]
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</StructureSection>
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[[Category: Vestergaard, B.]]
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[[Category: Buffalo rat]]
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[[Category: CA]]
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[[Category: Large Structures]]
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[[Category: glycoprotein]]
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[[Category: Gajhede, M]]
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[[Category: ion transport]]
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[[Category: Kastrup, J S]]
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[[Category: ionic channel]]
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[[Category: Naur, P]]
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[[Category: ionotropic glutamate receptors]]
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[[Category: Vestergaard, B]]
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[[Category: ligand-binding core]]
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[[Category: Glycoprotein]]
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[[Category: membrane]]
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[[Category: Ion transport]]
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[[Category: membrane protein]]
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[[Category: Ionic channel]]
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[[Category: postsynaptic membrane]]
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[[Category: Ionotropic glutamate receptor]]
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[[Category: receptor]]
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[[Category: Ligand-binding core]]
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[[Category: transmembrane]]
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[[Category: Membrane]]
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[[Category: transport]]
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[[Category: Membrane protein]]
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[[Category: Postsynaptic membrane]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 18:44:16 2007''
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[[Category: Receptor]]
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[[Category: Transmembrane]]
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[[Category: Transport]]

Current revision

Structure of the ligand-binding core of the ionotropic glutamate receptor-like GluRdelta2 in the apo form

PDB ID 2v3t

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