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| | <StructureSection load='4jp2' size='340' side='right'caption='[[4jp2]], [[Resolution|resolution]] 1.15Å' scene=''> | | <StructureSection load='4jp2' size='340' side='right'caption='[[4jp2]], [[Resolution|resolution]] 1.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jp2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JP2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jp2]] is a 1 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=4JP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JP2 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jp3|4jp3]]</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=4jp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jp2 OCA], [https://pdbe.org/4jp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jp2 RCSB], [https://www.ebi.ac.uk/pdbsum/4jp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jp2 ProSAT]</span></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=4jp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jp2 OCA], [http://pdbe.org/4jp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jp2 RCSB], [http://www.ebi.ac.uk/pdbsum/4jp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jp2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q53W82_THET8 Q53W82_THET8] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thermus thermophilus]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Kunishima, N]] | + | [[Category: Kunishima N]] |
| - | [[Category: Lokanath, N K]] | + | [[Category: Lokanath NK]] |
| - | [[Category: Pampa, K J]] | + | [[Category: Pampa KJ]] |
| - | [[Category: Rai, V Ravishnkar]] | + | [[Category: Ravishnkar Rai V]] |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| Structural highlights
Function
Q53W82_THET8
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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