5xwc

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Current revision (10:20, 27 March 2024) (edit) (undo)
 
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<StructureSection load='5xwc' size='340' side='right'caption='[[5xwc]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='5xwc' size='340' side='right'caption='[[5xwc]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5xwc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XWC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XWC FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5xwc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XWC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XWC 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=2IT:(2Z)-2-iminopentanedioic+acid'>2IT</scene>, <scene name='pdbligand=8GL:(2S)-2-azanyl-2-oxidanyl-pentanedioic+acid'>8GL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xwc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xwc OCA], [http://pdbe.org/5xwc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xwc RCSB], [http://www.ebi.ac.uk/pdbsum/5xwc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xwc ProSAT]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2IT:(2Z)-2-iminopentanedioic+acid'>2IT</scene>, <scene name='pdbligand=8GL:(2S)-2-azanyl-2-oxidanyl-pentanedioic+acid'>8GL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=5xwc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xwc OCA], [https://pdbe.org/5xwc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xwc RCSB], [https://www.ebi.ac.uk/pdbsum/5xwc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xwc ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/B6V7E4_ASPNG B6V7E4_ASPNG]
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Glutamate dehydrogenase (GDH) is a key enzyme connecting carbon and nitrogen metabolism in all living organisms. Despite extensive studies on GDHs from both prokaryotic and eukaryotic organisms in the last 40 years, the structural basis of the catalytic features of this enzyme remains incomplete. This study reports the structural basis of the GDH catalytic mechanism and allosteric behavior. We determined the first high-resolution crystal structures of glutamate dehydrogenase from the fungus Aspergillus niger (AnGDH), a unique NADP(+)-dependent allosteric enzyme that is forward inhibited by the formation of mixed disulfide. We determined the structures of the active enzyme in its apo form and in binary/ternary complexes with bound substrate (alpha- ketoglutarate), inhibitor (isophthalate), coenzyme (NADPH), or two reaction intermediates (alpha-iminoglutarate and 2-amino-2-hydroxyglutarate). The structure of the forward-inhibited enzyme (fiAnGDH) was also determined. The hexameric AnGDH had three open subunits at one side and three partially closed protomers at the other, a configuration not previously been reported. The AnGDH hexamers having subunits with different conformations indicated that its alpha-ketoglutarate-dependent homotropic cooperativity follows the Monod-Wyman-Changeux (MWC) model. Moreover, the position of the water attached to Asp154 and Gly153 defined the previously unresolved ammonium ion-binding pocket, and the binding site for the 2'-phosphate group of the coenzyme was also better defined by our structural data. Additional structural and mutagenesis experiments identified the residues essential for coenzyme recognition. This study reveals the structural features responsible for positioning alpha-ketoglutarate, NADPH, ammonium ion, and the reaction intermediates in the GDH active site.
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Structural basis for the catalytic mechanism and alpha-ketoglutarate cooperativity of glutamate dehydrogenase.,Prakash P, Punekar NS, Bhaumik P J Biol Chem. 2018 Mar 14. pii: RA117.000149. doi: 10.1074/jbc.RA117.000149. PMID:29540480<ref>PMID:29540480</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5xwc" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Glutamate dehydrogenase 3D structures|Glutamate dehydrogenase 3D structures]]
*[[Glutamate dehydrogenase 3D structures|Glutamate dehydrogenase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Aspergillus niger]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Bhaumik, P]]
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[[Category: Bhaumik P]]
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[[Category: Prakash, P]]
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[[Category: Prakash P]]
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[[Category: Punekar, N S]]
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[[Category: Punekar NS]]
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[[Category: 2-amino-2-hydroxyglutarate]]
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[[Category: Alpha-iminoglutarate]]
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[[Category: Aspergillus niger]]
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[[Category: Coenzyme]]
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[[Category: Glutamate dehydrogenase]]
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[[Category: Nadp]]
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[[Category: Oxidoreductase]]
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[[Category: Reaction intermediate]]
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Current revision

Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-iminoglutarate, 2-amino-2-hydroxyglutarate and NADP

PDB ID 5xwc

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OCA

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