2dtx
From Proteopedia
(Difference between revisions)
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==Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with D-mannose== | ==Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with D-mannose== | ||
| - | <StructureSection load='2dtx' size='340' side='right'caption='[[2dtx]]' scene=''> | + | <StructureSection load='2dtx' size='340' side='right'caption='[[2dtx]], [[Resolution|resolution]] 1.60Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dtx]] 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=2DTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTX FirstGlance]. <br> |
| - | </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=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [https://pdbe.org/2dtx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [https://www.ebi.ac.uk/pdbsum/2dtx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtx ProSAT]</span></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]] 1.6Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <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=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [https://pdbe.org/2dtx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [https://www.ebi.ac.uk/pdbsum/2dtx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtx ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q9HK51_THEAC Q9HK51_THEAC] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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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=2dtx ConSurf]. | </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=2dtx ConSurf]. | ||
<div style="clear:both"></div> | <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. | ||
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| + | 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> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2dtx" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[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]] | ||
Revision as of 08:30, 25 October 2023
Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with D-mannose
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