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| | <StructureSection load='4bht' size='340' side='right'caption='[[4bht]], [[Resolution|resolution]] 2.50Å' scene=''> | | <StructureSection load='4bht' size='340' side='right'caption='[[4bht]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4bht]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yfg 2yfg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BHT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BHT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4bht]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2yfg 2yfg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BHT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BHT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 2.5Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NADP(+)) Glutamate dehydrogenase (NADP(+))], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.4 1.4.1.4] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=4bht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bht OCA], [https://pdbe.org/4bht PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bht RCSB], [https://www.ebi.ac.uk/pdbsum/4bht PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bht ProSAT]</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=4bht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bht OCA], [https://pdbe.org/4bht PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bht RCSB], [https://www.ebi.ac.uk/pdbsum/4bht PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bht ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DHE4_ECOLI DHE4_ECOLI]] Catalyzes the reversible oxidative deamination of glutamate to alpha-ketoglutarate and ammonia.<ref>PMID:235298</ref> <ref>PMID:241744</ref>
| + | [https://www.uniprot.org/uniprot/DHE4_ECOLI DHE4_ECOLI] Catalyzes the reversible oxidative deamination of glutamate to alpha-ketoglutarate and ammonia.<ref>PMID:235298</ref> <ref>PMID:241744</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Engel, P]] | + | [[Category: Engel P]] |
| - | [[Category: Khan, A]] | + | [[Category: Khan A]] |
| - | [[Category: Oliveira, T]] | + | [[Category: Oliveira T]] |
| - | [[Category: Sharkey, M]] | + | [[Category: Sharkey M]] |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
DHE4_ECOLI Catalyzes the reversible oxidative deamination of glutamate to alpha-ketoglutarate and ammonia.[1] [2]
Publication Abstract from PubMed
Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of l-glutamate to alpha-ketoglutarate using NAD+ and/or NADP+ as a cofactor. Subunits of homo-hexameric bacterial enzymes comprise a substrate-binding Domain I followed by a nucleotide binding Domain II. The reaction occurs in a catalytic cleft between the two domains. Although conserved residues in the nucleotide-binding domains of various dehydrogenases have been linked to cofactor preferences, the structural basis for specificity in the glutamate dehydrogenase (GDH) family remains poorly understood. Here, the refined crystal structure of Escherichia coli GDH in the absence of reactants is described at 2.5A resolution. Modelling of NADP+ in Domain II reveals the potential contribution of positively charged residues from a neighbouring alpha-helical hairpin to phosphate recognition. In addition, a serine residue that follows the P7 aspartate is presumed to form a hydrogen bond to the 2'-phosphate. Mutagenesis and kinetic analysis confirms the importance of these residues in NADP+ recognition. Surprisingly, one of the positively charged residues is conserved in all sequences of NAD+ dependent enzymes, but the conformations adopted by the corresponding regions in proteins whose structure has been solved preclude their contribution toward the co-ordination of the 2'-ribose phosphate of NADP+ . These studies clarify the sequence/structure relationships in bacterial glutamate dehydrogenases, revealing that identical residues may specify different coenzyme preferences, depending on the structural context. Primary sequence alone is therefore not a reliable guide for predicting coenzyme specificity. We also consider how it is possible for a single sequence to accommodate both coenzymes in the dual specificity GDHs of animals. This article is protected by copyright. All rights reserved.
Structure of NADP -dependent glutamate dehydrogenase from Escherichia coli: Reflections on the basis of coenzyme specificity in the family of glutamate dehydrogenases.,Sharkey MA, Oliveira TF, Engel PC, Khan AR FEBS J. 2013 Jul 23. doi: 10.1111/febs.12439. PMID:23879525[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Veronese FM, Boccu E, Conventi L. Glutamate dehydrogenase from Escherichia coli: induction, purification and properties of the enzyme. Biochim Biophys Acta. 1975 Feb 19;377(2):217-28. PMID:235298
- ↑ Sakamoto N, Kotre AM, Savageau MA. Glutamate dehydrogenase from Escherichia coli: purification and properties. J Bacteriol. 1975 Nov;124(2):775-83. PMID:241744
- ↑ Sharkey MA, Oliveira TF, Engel PC, Khan AR. Structure of NADP -dependent glutamate dehydrogenase from Escherichia coli: Reflections on the basis of coenzyme specificity in the family of glutamate dehydrogenases. FEBS J. 2013 Jul 23. doi: 10.1111/febs.12439. PMID:23879525 doi:10.1111/febs.12439
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