2ekq

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{{Seed}}
 
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[[Image:2ekq.png|left|200px]]
 
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==Structure of TT0495 protein from Thermus thermophilus==
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The line below this paragraph, containing "STRUCTURE_2ekq", creates the "Structure Box" on the page.
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<StructureSection load='2ekq' size='340' side='right'caption='[[2ekq]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<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>
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{{STRUCTURE_2ekq| PDB=2ekq | SCENE= }}
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q53W82_THET8 Q53W82_THET8]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ek/2ekq_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ekq ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Structure of TT0495 protein from Thermus thermophilus===
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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<ref>PMID:24699644</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==About this Structure==
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</div>
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2EKQ is a [[Single protein]] structure of 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=2EKQ OCA].
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<div class="pdbe-citations 2ekq" style="background-color:#fffaf0;"></div>
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[[Category: 2-deoxy-D-gluconate 3-dehydrogenase]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Thermus thermophilus]]
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__TOC__
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[[Category: Lokanath, N K.]]
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</StructureSection>
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[[Category: Pampa, K J.]]
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[[Category: Large Structures]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Gluconate dehydrogenase]]
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[[Category: Lokanath NK]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Pampa KJ]]
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[[Category: Nppsfa]]
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[[Category: Oxidoreductase]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 29 05:45:25 2008''
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Current revision

Structure of TT0495 protein from Thermus thermophilus

PDB ID 2ekq

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