7ecr

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Succinate and ADP-ribose

Structural highlights

7ecr is a 3 chain structure with sequence from Aspergillus terreus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.73Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T2D1F5_ASPTE

Publication Abstract from PubMed

Glutamate dehydrogenase (GDH) is a salient metabolic enzyme which catalyzes the NAD(+) - or NADP(+) -dependent reversible conversion of alpha-ketoglutarate (AKG) to l-glutamate; and thereby connects the carbon and nitrogen metabolism cycles in all living organisms. The function of GDH is extensively regulated by both metabolites (citrate, succinate, etc.) and non-metabolites (ATP, NADH, etc.) but sufficient molecular evidences are lacking to rationalize the inhibitory effects by the metabolites. We have expressed and purified NADP(+) -dependent Aspergillus terreus GDH (AtGDH) in recombinant form. Succinate, malonate, maleate, fumarate, and tartrate independently inhibit the activity of AtGDH to different extents. The crystal structures of AtGDH complexed with the dicarboxylic acid metabolites and the coenzyme NADPH have been determined. Although AtGDH structures are not complexed with substrate; surprisingly, they acquire super closed conformation like previously reported for substrate and coenzyme bound catalytically competent Aspergillus niger GDH (AnGDH). These dicarboxylic acid metabolites partially occupy the same binding pocket as substrate; but interact with varying polar interactions and the coenzyme NADPH binds to the Domain-II of AtGDH. The low inhibition potential of tartrate as compared to other dicarboxylic acid metabolites is due to its weaker interactions of carboxylate groups with AtGDH. Our results suggest that the length of carbon skeleton and positioning of the carboxylate groups of inhibitors between two conserved lysine residues at the GDH active site might be the determinants of their inhibitory potency. Molecular details on the dicarboxylic acid metabolites bound AtGDH active site architecture presented here would be applicable to GDHs in general.

Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites.,Godsora BKJ, Prakash P, Punekar NS, Bhaumik P Proteins. 2021 Nov 8. doi: 10.1002/prot.26276. PMID:34748226^[1]

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

References

↑ Godsora BKJ, Prakash P, Punekar NS, Bhaumik P. Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites. Proteins. 2021 Nov 8. doi: 10.1002/prot.26276. PMID:34748226 doi:http://dx.doi.org/10.1002/prot.26276

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/7ecr"

@@ Line 3: / Line 3: @@
 <StructureSection load='7ecr' size='340' side='right'caption='[[7ecr]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7ecr]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ECR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7ecr]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_terreus Aspergillus terreus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ECR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2R:[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+[(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>A2R</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 1.73&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5xvx|5xvx]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2R:[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+[(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>A2R</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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=7ecr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ecr OCA], [https://pdbe.org/7ecr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ecr RCSB], [https://www.ebi.ac.uk/pdbsum/7ecr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ecr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/T2D1F5_ASPTE T2D1F5_ASPTE]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 7ecr" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Glutamate dehydrogenase 3D structures|Glutamate dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Aspergillus terreus]]
 [[Category: Large Structures]]
-[[Category: Bhaumik, P]]
+[[Category: Bhaumik P]]
-[[Category: Godsora, B K.J]]
+[[Category: Godsora BKJ]]
-[[Category: Prakash, P]]
+[[Category: Prakash P]]
-[[Category: Punekar, N S]]
+[[Category: Punekar NS]]
-[[Category: Allostery]]
-[[Category: Aspergillus]]
-[[Category: Enzyme mechanism]]
-[[Category: Glutamate dehydrogenase]]
-[[Category: Oxidoreductase]]

7ecr

From Proteopedia

Current revision

Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Succinate and ADP-ribose

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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