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5xvi

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Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase

Structural highlights

5xvi is a 6 chain structure with sequence from Aspergillus niger. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B6V7E4_ASPNG

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Prakash P, Punekar NS, Bhaumik P. Structural basis for the catalytic mechanism and alpha-ketoglutarate cooperativity of glutamate dehydrogenase. J Biol Chem. 2018 Mar 14. pii: RA117.000149. doi: 10.1074/jbc.RA117.000149. PMID:29540480 doi:http://dx.doi.org/10.1074/jbc.RA117.000149

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5xvi"

Categories: Aspergillus niger | Large Structures | Bhaumik P | Prakash P | Punekar NS

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase==
-<StructureSection load='5xvi' size='340' side='right' caption='[[5xvi]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='5xvi' size='340' side='right'caption='[[5xvi]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xvi]] is a 6 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=5XVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XVI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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]] 2.8&#8491;</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=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [http://pdbe.org/5xvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [http://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [https://pdbe.org/5xvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [https://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/B6V7E4_ASPNG B6V7E4_ASPNG]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 19: @@
 </div>
 <div class="pdbe-citations 5xvi" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Glutamate dehydrogenase 3D structures|Glutamate dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: A. niger]]
+[[Category: Aspergillus niger]]
-[[Category: Bhaumik, P]]
+[[Category: Large Structures]]
-[[Category: Prakash, P]]
+[[Category: Bhaumik P]]
-[[Category: Punekar, N S]]
+[[Category: Prakash P]]
-[[Category: 2-oxoglutarate]]
+[[Category: Punekar NS]]
-[[Category: Allostery]]
-[[Category: Aspergillus]]
-[[Category: Dehydrogenase]]
-[[Category: Glutamate]]
-[[Category: Oxidoreductase]]

5xvi

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Current revision

Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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