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| | <StructureSection load='2ekq' size='340' side='right'caption='[[2ekq]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='2ekq' size='340' side='right'caption='[[2ekq]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2ekq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EKQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2ekq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EKQ FirstGlance]. <br> |
| - | </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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ekp|2ekp]]</div></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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-deoxy-D-gluconate_3-dehydrogenase 2-deoxy-D-gluconate 3-dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.125 1.1.1.125] </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=2ekq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ekq OCA], [https://pdbe.org/2ekq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ekq RCSB], [https://www.ebi.ac.uk/pdbsum/2ekq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ekq ProSAT], [https://www.topsan.org/Proteins/RSGI/2ekq TOPSAN]</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=2ekq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ekq OCA], [https://pdbe.org/2ekq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ekq RCSB], [https://www.ebi.ac.uk/pdbsum/2ekq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ekq ProSAT], [https://www.topsan.org/Proteins/RSGI/2ekq TOPSAN]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q53W82_THET8 Q53W82_THET8] |
| | == 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: 2-deoxy-D-gluconate 3-dehydrogenase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thet8]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Lokanath, N K]] | + | [[Category: Lokanath NK]] |
| - | [[Category: Pampa, K J]] | + | [[Category: Pampa KJ]] |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Gluconate dehydrogenase]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| Structural highlights
Function
Q53W82_THET8
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
2-Keto-3-deoxygluconate (KDG) is one of the important intermediates in pectin metabolism. An enzyme involved in this pathway, 3-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (DDGDH), has been identified which converts 2,5-diketo-3-deoxygluconate to KDG. The enzyme is a member of the short-chain dehydrogenase (SDR) family. To gain insight into the function of this enzyme at the molecular level, the first crystal structure of DDGDH from Thermus thermophilus HB8 has been determined in the apo form, as well as in complexes with the cofactor and with citrate, by X-ray diffraction methods. The crystal structures reveal a tight tetrameric oligomerization. The secondary-structural elements and catalytically important residues of the enzyme were highly conserved amongst the proteins of the NAD(P)-dependent SDR family. The DDGDH protomer contains a dinucleotide-binding fold which binds the coenzyme NAD(+) in an intersubunit cleft; hence, the observed oligomeric state might be important for the catalytic function. This enzyme prefers NAD(H) rather than NADP(H) as the physiological cofactor. A structural comparison of DDGDH with mouse lung carbonyl reductase suggests that a significant difference in the alpha-loop-alpha region of this enzyme is associated with the coenzyme specificity. The structural data allow a detailed understanding of the functional role of the conserved catalytic triad (Ser129-Tyr144-Lys148) in cofactor and substrate recognition, thus providing substantial insights into DDGDH catalysis. From analysis of the three-dimensional structure, intersubunit hydrophobic interactions were found to be important for enzyme oligomerization and thermostability.
The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8.,Pampa KJ, Lokanath NK, Kunishima N, Rai RV Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):994-1004. doi:, 10.1107/S1399004713034925. Epub 2014 Mar 19. PMID:24699644[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Pampa KJ, Lokanath NK, Kunishima N, Rai RV. The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8. Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):994-1004. doi:, 10.1107/S1399004713034925. Epub 2014 Mar 19. PMID:24699644 doi:http://dx.doi.org/10.1107/S1399004713034925
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