2dtx - Revision history

OCA at 08:30, 25 October 2023

OCA — Wed, 25 Oct 2023 08:30:03 GMT

←Older revision		Revision as of 08:30, 25 October 2023
Line 1:		Line 1:

	==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]]
Line 16:		Line 20:
	</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.
		+
		+	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>
		+
		+	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]]

OCA at 10:35, 17 February 2021

OCA — Wed, 17 Feb 2021 10:35:32 GMT

←Older revision		Revision as of 10:35, 17 February 2021
Line 1:		Line 1:

	==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]]~~, [[Resolution\|resolution]] 1.60Å~~' scene=''>	+	<StructureSection load='2dtx' size='340' side='right'caption='[[2dtx]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[2dtx]] is a 2 chain structure with sequence from [http://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=2DTX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DTX FirstGlance]. <br>	+	<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>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</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>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dtd\|2dtd]], [[2dte\|2dte]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ta0754 ([http://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'>[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] </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=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [~~http~~://pdbe.org/2dtx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dtx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtx ProSAT]</span></td></tr>	+
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 20:		Line 16:
	</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.
-
-	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>
-
-	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: Nishiya, Y]]	+	[[Category: Large Structures]]
-	[[Category: Tamura, N]]	+	[[Category: Nishiya Y]]
-	[[Category: Tamura, T]]	+	[[Category: Tamura N]]
-	[[Category: Yasutake, Y]]	+	[[Category: Tamura T]]
-	~~[[Category: Oxidoreductase]]~~	+	[[Category: Yasutake Y]]
-	~~[[Category: Rossmann fold~~]]	+

OCA at 06:46, 6 June 2018

OCA — Wed, 06 Jun 2018 06:46:57 GMT

←Older revision		Revision as of 06:46, 6 June 2018
Line 1:		Line 1:
		+
	==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]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2dtx' size='340' side='right' caption='[[2dtx]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ta0754 ([http://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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ta0754 ([http://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'>[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] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [http://pdbe.org/2dtx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [http://www.ebi.ac.uk/pdbsum/2dtx PDBsum]</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=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [http://pdbe.org/2dtx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [http://www.ebi.ac.uk/pdbsum/2dtx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtx ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtx_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtx_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 04:11, 8 February 2016

OCA — Mon, 08 Feb 2016 04:11:33 GMT

←Older revision		Revision as of 04:11, 8 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ 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;">		<div style="background-color:#fffaf0;">

OCA at 07:44, 10 September 2015

OCA — Thu, 10 Sep 2015 07:44:04 GMT

←Older revision		Revision as of 07:44, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2dtx' size='340' side='right' caption='[[2dtx]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2dtx' size='340' side='right' caption='[[2dtx]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dtx]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dtx]] is a 2 chain structure with sequence from [http://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=2DTX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <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"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <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">[[2dtd\|2dtd]], [[2dte\|2dte]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dtd\|2dtd]], [[2dte\|2dte]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ta0754 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma ~~acidophilum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ta0754 ([http://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'>[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] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [http://www.ebi.ac.uk/pdbsum/2dtx PDBsum]</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=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [http://pdbe.org/2dtx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [http://www.ebi.ac.uk/pdbsum/2dtx PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2dtx" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Thermoplasma acidophilum]]
	[[Category: Nishiya, Y]]		[[Category: Nishiya, Y]]
	[[Category: Tamura, N]]		[[Category: Tamura, N]]

OCA at 17:51, 15 January 2015

OCA — Thu, 15 Jan 2015 17:51:13 GMT

←Older revision		Revision as of 17:51, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dtx]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTX FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dtx]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dtd\|2dtd]], [[2dte\|2dte]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dtd\|2dtd]], [[2dte\|2dte]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ta0754 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ta0754 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [http://www.ebi.ac.uk/pdbsum/2dtx PDBsum]</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=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [http://www.ebi.ac.uk/pdbsum/2dtx PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Thermoplasma acidophilum]]		[[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: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

OCA at 00:57, 30 September 2014

OCA — Tue, 30 Sep 2014 00:57:32 GMT

←Older revision		Revision as of 00:57, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2dtx.~~png~~\|~~left~~\|200px]]	+	==Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with D-mannose==
		+	<StructureSection load='2dtx' size='340' side='right' caption='[[2dtx]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dtx]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DTX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dtd\|2dtd]], [[2dte\|2dte]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ta0754 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dtx RCSB], [http://www.ebi.ac.uk/pdbsum/2dtx PDBsum]</span></td></tr>
		+	<table>
		+	== 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/2dtx_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata 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.

-	~~{{STRUCTURE_2dtx\| PDB=2dtx \| SCENE= }}~~	+	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>

-	~~===Structure~~ of ~~Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with D-mannose===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17300803}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2dtx]] is a 2 chain structure with sequence from [http://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].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017300803<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermoplasma acidophilum]]		[[Category: Thermoplasma acidophilum]]
	[[Category: Nishiya, Y.]]		[[Category: Nishiya, Y.]]

OCA: Protected "2dtx" [edit=sysop:move=sysop]

OCA — Sun, 06 Jan 2013 10:15:48 GMT

Protected "2dtx" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:15, 6 January 2013

OCA at 10:15, 6 January 2013

OCA — Sun, 06 Jan 2013 10:15:43 GMT

←Older revision		Revision as of 10:15, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2dtx.png\|left\|200px]]		[[Image:2dtx.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2dtx", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2dtx\| PDB=2dtx \| SCENE= }}		{{STRUCTURE_2dtx\| PDB=2dtx \| SCENE= }}

	===Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with D-mannose===		===Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with D-mannose===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17300803}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17300803 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17300803}}		{{ABSTRACT_PUBMED_17300803}}

	==About this Structure==		==About this Structure==
-	~~2DTX~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://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].	+	[[2dtx]] is a 2 chain structure with sequence from [http://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].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17300803~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017300803</ref><references group="xtra"/>
	[[Category: Thermoplasma acidophilum]]		[[Category: Thermoplasma acidophilum]]
	[[Category: Nishiya, Y.]]		[[Category: Nishiya, Y.]]
Line 29:		Line 17:
	[[Category: Tamura, T.]]		[[Category: Tamura, T.]]
	[[Category: Yasutake, Y.]]		[[Category: Yasutake, Y.]]
		+	[[Category: Oxidoreductase]]
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:43:06 2009''

OCA at 16:43, 16 February 2009

OCA — Mon, 16 Feb 2009 16:43:09 GMT

←Older revision		Revision as of 16:43, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2DTX is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://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].	+	2DTX is a 2 chains structure of sequences from [http://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].

	==Reference==		==Reference==
-	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:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17300803 17300803]~~	+	<ref group="xtra">PMID:17300803</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Thermoplasma acidophilum]]		[[Category: Thermoplasma acidophilum]]
	[[Category: Nishiya, Y.]]		[[Category: Nishiya, Y.]]
Line 32:		Line 31:
	[[Category: Rossmann fold]]		[[Category: Rossmann fold]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 22~~:59:~~20 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:43:06 2009''