2dtd: Difference between revisions
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==Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in ligand-free form== | ==Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in ligand-free form== | ||
<StructureSection load='2dtd' size='340' side='right' caption='[[2dtd]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='2dtd' size='340' side='right'caption='[[2dtd]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2dtd]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2dtd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dte|2dte]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dte|2dte]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ta0754 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ta0754 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucose_1-dehydrogenase_(NAD(+)) Glucose 1-dehydrogenase (NAD(+))], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.118 1.1.1.118] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Nishiya, Y]] | [[Category: Nishiya, Y]] | ||
[[Category: Tamura, N]] | [[Category: Tamura, N]] | ||
Revision as of 14:37, 10 February 2021
Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in ligand-free formStructure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in ligand-free form
Structural highlights
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 PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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