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| | <StructureSection load='1v9l' size='340' side='right'caption='[[1v9l]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='1v9l' size='340' side='right'caption='[[1v9l]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1v9l]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Dsm_4184 Dsm 4184]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9L FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1v9l]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_islandicum Pyrobaculum islandicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9L FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.8Å</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 Glutamate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.2 1.4.1.2] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=1v9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9l OCA], [https://pdbe.org/1v9l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9l RCSB], [https://www.ebi.ac.uk/pdbsum/1v9l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9l 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=1v9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9l OCA], [https://pdbe.org/1v9l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9l RCSB], [https://www.ebi.ac.uk/pdbsum/1v9l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9l ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q9Y8I4_PYRIS Q9Y8I4_PYRIS] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Dsm 4184]] | |
| - | [[Category: Glutamate dehydrogenase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bhuiya, M W]] | + | [[Category: Pyrobaculum islandicum]] |
| - | [[Category: Imagawa, T]] | + | [[Category: Bhuiya MW]] |
| - | [[Category: Katunuma, N]] | + | [[Category: Imagawa T]] |
| - | [[Category: Ohshima, T]] | + | [[Category: Katunuma N]] |
| - | [[Category: Sakuraba, H]] | + | [[Category: Ohshima T]] |
| - | [[Category: Tsuge, H]] | + | [[Category: Sakuraba H]] |
| - | [[Category: Oxidoreductase]]
| + | [[Category: Tsuge H]] |
| - | [[Category: Protein-nad complex]]
| + | |
| Structural highlights
Function
Q9Y8I4_PYRIS
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The extremely thermostable NAD-dependent glutamate dehydrogenase (NAD-GluDH) from Pyrobaculum islandicum, a member of the Crenarchaeota, was crystallized, and its 3D structure has been determined by X-ray diffraction methods. The homohexameric structure of Pb. islandicum glutamate dehydrogenase (Pis-GluDH) was solved and refined at a resolution of 2.9A with a crystallographic R-factor of 19.9% (Rfree 26.0%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. The secondary structural elements and catalytically important residues of the enzyme were highly conserved among the NAD(P)-dependent GluDHs from other sources. A structural comparison of Pis-GluDH with other NAD(P)-dependent GluDHs suggests that a significant difference in the alpha8-loop-alpha9 region of this enzyme is associated with its coenzyme specificity. From the analysis of the 3D structure, hydrophobic interactions between intersubunits were found to be important features for the enzyme oligomerization. It has been reported that Pis-GluDH is highly thermostable, like the GluDH of the hyperthermophilic archaeum Pyrococcus furiosus, and the increase in the intersubunit ion pair networks is responsible for the extreme thermostability of the Pc. furiosus enzyme. However, the number of intersubunit ion pairs in the Pis-GluDH molecules is much smaller than those of the Pc. furiosus GluDH. The number of hydrophobic interactions at the intersubunit interfaces were increased and responsible for the extremely high thermostability. This indicates that the major molecular strategy for high thermostability of the GluDHs may be different for each hyperthermophile.
The first crystal structure of hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum.,Bhuiya MW, Sakuraba H, Ohshima T, Imagawa T, Katunuma N, Tsuge H J Mol Biol. 2005 Jan 14;345(2):325-37. PMID:15571725[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Bhuiya MW, Sakuraba H, Ohshima T, Imagawa T, Katunuma N, Tsuge H. The first crystal structure of hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum. J Mol Biol. 2005 Jan 14;345(2):325-37. PMID:15571725 doi:10.1016/j.jmb.2004.10.063
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