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3jd4

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Glutamate dehydrogenase in complex with NADH and GTP, closed conformation

3jd4, resolution 3.40Å

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@@ Line 3: / Line 3: @@
 <SX load='3jd4' size='340' side='right' viewer='molstar' caption='[[3jd4]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3jd4]] is a 6 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=3JD4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3JD4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3jd4]] is a 6 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=3JD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JD4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3jcz|3jcz]], [[3jd0|3jd0]], [[3jd1|3jd1]], [[3jd2|3jd2]], [[3jd3|3jd3]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></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=3jd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jd4 OCA], [https://pdbe.org/3jd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jd4 RCSB], [https://www.ebi.ac.uk/pdbsum/3jd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jd4 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3jd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jd4 OCA], [http://pdbe.org/3jd4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jd4 RCSB], [http://www.ebi.ac.uk/pdbsum/3jd4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jd4 ProSAT]</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>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Cryo-electron microscopy (cryo-EM) methods are now being used to determine structures at near-atomic resolution and have great promise in molecular pharmacology, especially in the context of mapping the binding of small-molecule ligands to protein complexes that display conformational flexibility. We illustrate this here using glutamate dehydrogenase (GDH), a 336-kDa metabolic enzyme that catalyzes the oxidative deamination of glutamate. Dysregulation of GDH leads to a variety of metabolic and neurologic disorders. Here, we report near-atomic resolution cryo-EM structures, at resolutions ranging from 3.2 A to 3.6 A for GDH complexes, including complexes for which crystal structures are not available. We show that the binding of the coenzyme NADH alone or in concert with GTP results in a binary mixture in which the enzyme is in either an "open" or "closed" state. Whereas the structure of NADH in the active site is similar between the open and closed states, it is unexpectedly different at the regulatory site. Our studies thus demonstrate that even in instances when there is considerable structural information available from X-ray crystallography, cryo-EM methods can provide useful complementary insights into regulatory mechanisms for dynamic protein complexes.
-Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.,Borgnia MJ, Banerjee S, Merk A, Matthies D, Bartesaghi A, Rao P, Pierson J, Earl LA, Falconieri V, Subramaniam S, Milne JL Mol Pharmacol. 2016 Jun;89(6):645-51. doi: 10.1124/mol.116.103382. Epub 2016 Apr , 1. PMID:27036132<ref>PMID:27036132</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3jd4" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 29: / Line 19: @@
 [[Category: Bos taurus]]
 [[Category: Large Structures]]
-[[Category: Banerjee, S]]
+[[Category: Banerjee S]]
-[[Category: Bartesaghi, A]]
+[[Category: Bartesaghi A]]
-[[Category: Borgnia, M J]]
+[[Category: Borgnia MJ]]
-[[Category: Earl, L A]]
+[[Category: Earl LA]]
-[[Category: Falconieri, V]]
+[[Category: Falconieri V]]
-[[Category: Matthies, D]]
+[[Category: Matthies D]]
-[[Category: Merk, A]]
+[[Category: Merk A]]
-[[Category: Milne, J L.S]]
+[[Category: Milne JLS]]
-[[Category: Pierson, J]]
+[[Category: Pierson J]]
-[[Category: Rao, P]]
+[[Category: Rao P]]
-[[Category: Subramaniam, S]]
+[[Category: Subramaniam S]]
-[[Category: Glutamate metabolism]]
-[[Category: Mitochondria]]
-[[Category: Oxidoreductase]]

3jd4

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Glutamate dehydrogenase in complex with NADH and GTP, closed conformation

Structural highlights

Function

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