2dtd: Difference between revisions

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OCA

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-[[Image:2dtd.gif|left|200px]]<br /><applet load="2dtd" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2dtd, resolution 2.10&Aring;" />
-'''Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in ligand-free form'''<br />
-==Overview==
+==Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in ligand-free form==
-The d-aldohexose dehydrogenase from the thermoacidophilic archaea, Thermoplasma acidophilum (AldT) belongs to the short-chain, dehydrogenase/reductase (SDR) superfamily and catalyzes the oxidation of, several monosaccharides with a preference for NAD(+) rather than NADP(+), as a cofactor. It has been found that AldT is a unique enzyme that, exhibits the highest dehydrogenase activity against d-mannose. Here, we, describe the crystal structures of AldT in ligand-free form, in complex, with NADH, and in complex with the substrate d-mannose, at 2.1 A, 1.65 A, and 1.6 A resolution, respectively. The AldT subunit forms a typical SDR, fold with an unexpectedly long C-terminal tail and assembles into an, intertwined tetramer. The d-mannose complex structure reveals that Glu84, interacts with the axial C2 hydroxyl group of the bound d-mannose., Structural comparison with Bacillus megaterium glucose dehydrogenase, (BmGlcDH) suggests that the conformation of the glutamate side-chain is, crucial for discrimination between d-mannose and its C2 epimer d-glucose, and the conformation of the glutamate side-chain depends on the spatial, arrangement of nearby hydrophobic residues that do not directly interact, with the substrate. Elucidation of the d-mannose recognition mechanism of, AldT further provides structural insights into the unique substrate, selectivity of AldT. Finally, we show that the extended C-terminal tail, completely shuts the substrate-binding pocket of the neighboring subunit, both in the presence and absence of substrate. The elaborate inter-subunit, interactions between the C-terminal tail and the entrance of the, substrate-binding pocket imply that the tail may play a pivotal role in, the enzyme activity.
+<StructureSection load='2dtd' size='340' side='right'caption='[[2dtd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2dtd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2dtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtd OCA], [https://pdbe.org/2dtd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtd RCSB], [https://www.ebi.ac.uk/pdbsum/2dtd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9HK51_THEAC Q9HK51_THEAC]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2dtd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The D-aldohexose dehydrogenase from the thermoacidophilic archaea Thermoplasma acidophilum (AldT) belongs to the short-chain dehydrogenase/reductase (SDR) superfamily and catalyzes the oxidation of several monosaccharides with a preference for NAD(+) rather than NADP(+) as a cofactor. It has been found that AldT is a unique enzyme that exhibits the highest dehydrogenase activity against D-mannose. Here, we describe the crystal structures of AldT in ligand-free form, in complex with NADH, and in complex with the substrate D-mannose, at 2.1 A, 1.65 A, and 1.6 A resolution, respectively. The AldT subunit forms a typical SDR fold with an unexpectedly long C-terminal tail and assembles into an intertwined tetramer. The D-mannose complex structure reveals that Glu84 interacts with the axial C2 hydroxyl group of the bound D-mannose. Structural comparison with Bacillus megaterium glucose dehydrogenase (BmGlcDH) suggests that the conformation of the glutamate side-chain is crucial for discrimination between D-mannose and its C2 epimer D-glucose, and the conformation of the glutamate side-chain depends on the spatial arrangement of nearby hydrophobic residues that do not directly interact with the substrate. Elucidation of the D-mannose recognition mechanism of AldT further provides structural insights into the unique substrate selectivity of AldT. Finally, we show that the extended C-terminal tail completely shuts the substrate-binding pocket of the neighboring subunit both in the presence and absence of substrate. The elaborate inter-subunit interactions between the C-terminal tail and the entrance of the substrate-binding pocket imply that the tail may play a pivotal role in the enzyme activity.
-==About this Structure==
+Structural insights into unique substrate selectivity of Thermoplasma acidophilum D-aldohexose dehydrogenase.,Yasutake Y, Nishiya Y, Tamura N, Tamura T J Mol Biol. 2007 Apr 6;367(4):1034-46. Epub 2007 Jan 16. PMID:17300803<ref>PMID:17300803</ref>
-DTD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glucose_1-dehydrogenase_(NAD(+)) Glucose 1-dehydrogenase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.118 1.1.1.118] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTD OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural Insights into Unique Substrate Selectivity of Thermoplasma acidophilumd-Aldohexose Dehydrogenase., Yasutake Y, Nishiya Y, Tamura N, Tamura T, J Mol Biol. 2007 Apr 6;367(4):1034-46. Epub 2007 Jan 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17300803 17300803]
+</div>
-[[Category: Glucose 1-dehydrogenase (NAD(+))]]
+<div class="pdbe-citations 2dtd" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermoplasma acidophilum]]
-[[Category: Nishiya, Y.]]
+[[Category: Nishiya Y]]
-[[Category: Tamura, N.]]
+[[Category: Tamura N]]
-[[Category: Tamura, T.]]
+[[Category: Tamura T]]
-[[Category: Yasutake, Y.]]
+[[Category: Yasutake Y]]
-[[Category: SO4]]
-[[Category: rossmann fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 19:11:43 2008''