1nr7: Difference between revisions

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 ==Crystal structure of apo bovine glutamate dehydrogenase==
-<StructureSection load='1nr7' size='340' side='right' caption='[[1nr7]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+<StructureSection load='1nr7' size='340' side='right'caption='[[1nr7]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nr7]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NR7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NR7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1nr7]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NR7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NR7 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1l1f|1l1f]], [[1nqt|1nqt]], [[1nr1|1nr1]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NAD(P)(+)) Glutamate dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.3 1.4.1.3] </span></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=1nr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nr7 OCA], [https://pdbe.org/1nr7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nr7 RCSB], [https://www.ebi.ac.uk/pdbsum/1nr7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nr7 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nr7 OCA], [http://pdbe.org/1nr7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nr7 RCSB], [http://www.ebi.ac.uk/pdbsum/1nr7 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DHE3_BOVIN DHE3_BOVIN]] May be involved in learning and memory reactions by increasing the turnover of the excitatory neurotransmitter glutamate (By similarity).<ref>PMID:14659072</ref>
+[https://www.uniprot.org/uniprot/DHE3_BOVIN DHE3_BOVIN] May be involved in learning and memory reactions by increasing the turnover of the excitatory neurotransmitter glutamate (By similarity).<ref>PMID:14659072</ref>
 == 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/nr/1nr7_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nr/1nr7_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 19: @@
 </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=1nr7 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Glutamate dehydrogenase (GDH) is found in all organisms and catalyzes the reversible oxidative deamination of L-glutamate to 2-oxoglutarate. Unlike GDH from bacteria, mammalian GDH exhibits negative cooperativity with respect to coenzyme, activation by ADP, and inhibition by GTP. Presented here are the structures of apo bovine GDH, bovine GDH complexed with ADP, and the R463A mutant form of human GDH (huGDH) that is insensitive to ADP activation. In the absence of active site ligands, the catalytic cleft is in the open conformation, and the hexamers form long polymers in the crystal cell with more interactions than found in the abortive complex crystals. This is consistent with the fact that ADP promotes aggregation in solution. ADP is shown to bind to the second, inhibitory, NADH site yet causes activation. The beta-phosphates of the bound ADP interact with R459 (R463 in huGDH) on the pivot helix. The structure of the ADP-resistant, R463A mutant of human GDH is identical to native GDH with the exception of the truncated side chain on the pivot helix. Together, these results strongly suggest that ADP activates by facilitating the opening of the catalytic cleft. From alignment of GDH from various sources, it is likely that the antenna evolved in the protista prior to the formation of purine regulatory sites. This suggests that there was some selective advantage of the antenna itself and that animals evolved new functions for GDH through the addition of allosteric regulation.
-Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation.,Banerjee S, Schmidt T, Fang J, Stanley CA, Smith TJ Biochemistry. 2003 Apr 1;42(12):3446-56. PMID:12653548<ref>PMID:12653548</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1nr7" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Glutamate dehydrogenase|Glutamate dehydrogenase]]
+*[[Glutamate dehydrogenase 3D structures|Glutamate dehydrogenase 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 27: @@
 </StructureSection>
 [[Category: Bos taurus]]
-[[Category: Banerjee, S]]
+[[Category: Large Structures]]
-[[Category: Fang, J]]
+[[Category: Banerjee S]]
-[[Category: Schmidt, T]]
+[[Category: Fang J]]
-[[Category: Smith, T J]]
+[[Category: Schmidt T]]
-[[Category: Stanley, C A]]
+[[Category: Smith TJ]]
-[[Category: Apo bovine glutamate dehydrogenase regulation allostery]]
+[[Category: Stanley CA]]
-[[Category: Oxidoreductase]]