4tvu - Revision history

OCA at 15:17, 8 November 2023

2023-11-08T15:17:57Z

←Older revision		Revision as of 15:17, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tvu]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TVU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tvu]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TVU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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]] 2.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4tvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvu OCA], [https://pdbe.org/4tvu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tvu RCSB], [https://www.ebi.ac.uk/pdbsum/4tvu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvu ProSAT]</span></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=4tvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvu OCA], [https://pdbe.org/4tvu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tvu RCSB], [https://www.ebi.ac.uk/pdbsum/4tvu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvu ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:58, 15 March 2023

2023-03-15T10:58:05Z

←Older revision		Revision as of 10:58, 15 March 2023
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	<StructureSection load='4tvu' size='340' side='right'caption='[[4tvu]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4tvu' size='340' side='right'caption='[[4tvu]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4tvu]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Deira Deira~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4TVU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4tvu]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TVU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Maltose_alpha-D-glucosyltransferase Maltose alpha-D-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.16 5.4.99.16] </span></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=4tvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvu OCA], [https://pdbe.org/4tvu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tvu RCSB], [https://www.ebi.ac.uk/pdbsum/4tvu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvu ProSAT]</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=4tvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvu OCA], [~~http~~://pdbe.org/4tvu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4tvu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4tvu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvu ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/I3NX86_DEIRA I3NX86_DEIRA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deira~~]]	+	[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Maltose alpha-D-glucosyltransferase]]~~	+	[[Category: Chow SY]]
-	[[Category: Chow~~, S Y~~]]	+	[[Category: Liaw SH]]
-	[[Category: Liaw~~, S H~~]]	+	[[Category: Lin YT]]
-	[[Category: Lin~~, Y T~~]]	+	[[Category: Wang YL]]
-	[[Category: Wang~~, Y L]]~~	+
-	~~[[Category: Glycoside hydrolase family 13]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Trehalose synthase]]~~	+
-	~~[[Category: Tris complex~~]]	+

OCA at 14:41, 10 May 2019

2019-05-10T14:41:24Z

←Older revision		Revision as of 14:41, 10 May 2019
Line 1:		Line 1:

	==Crystal structure of trehalose synthase from Deinococcus radiodurans reveals a closed conformation for catalysis of the intramolecular isomerization==		==Crystal structure of trehalose synthase from Deinococcus radiodurans reveals a closed conformation for catalysis of the intramolecular isomerization==
-	<StructureSection load='4tvu' size='340' side='right' caption='[[4tvu]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='4tvu' size='340' side='right'caption='[[4tvu]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4tvu]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4tvu]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Maltose_alpha-D-glucosyltransferase Maltose alpha-D-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.16 5.4.99.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Maltose_alpha-D-glucosyltransferase Maltose alpha-D-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.16 5.4.99.16] </span></td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deira]]
		+	[[Category: Large Structures]]
	[[Category: Maltose alpha-D-glucosyltransferase]]		[[Category: Maltose alpha-D-glucosyltransferase]]
	[[Category: Chow, S Y]]		[[Category: Chow, S Y]]

OCA at 13:40, 5 August 2016

2016-08-05T13:40:40Z

←Older revision		Revision as of 13:40, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of trehalose synthase from Deinococcus radiodurans reveals a closed conformation for catalysis of the intramolecular isomerization==		==Crystal structure of trehalose synthase from Deinococcus radiodurans reveals a closed conformation for catalysis of the intramolecular isomerization==
	<StructureSection load='4tvu' size='340' side='right' caption='[[4tvu]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4tvu' size='340' side='right' caption='[[4tvu]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Maltose_alpha-D-glucosyltransferase Maltose alpha-D-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.16 5.4.99.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Maltose_alpha-D-glucosyltransferase Maltose alpha-D-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.16 5.4.99.16] </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=4tvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tvu RCSB], [http://www.ebi.ac.uk/pdbsum/4tvu 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=4tvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvu OCA], [http://pdbe.org/4tvu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tvu RCSB], [http://www.ebi.ac.uk/pdbsum/4tvu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tvu ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4tvu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:37, 17 December 2014

2014-12-17T12:37:43Z

←Older revision		Revision as of 12:37, 17 December 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of trehalose synthase from Deinococcus radiodurans reveals a closed conformation for catalysis of the intramolecular isomerization==
		+	<StructureSection load='4tvu' size='340' side='right' caption='[[4tvu]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4tvu]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TVU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TVU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Maltose_alpha-D-glucosyltransferase Maltose alpha-D-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.16 5.4.99.16] </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=4tvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tvu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tvu RCSB], [http://www.ebi.ac.uk/pdbsum/4tvu PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Trehalose synthase catalyzes the simple conversion of the inexpensive maltose into trehalose with a side reaction of hydrolysis. Here, the crystal structures of the wild type and the N253A mutant of Deinococcus radiodurans trehalose synthase (DrTS) in complex with the inhibitor Tris are reported. DrTS consists of a catalytic (beta/alpha)8 barrel, subdomain B, a C-terminal beta domain and two TS-unique subdomains (S7 and S8). The C-terminal domain and S8 contribute the majority of the dimeric interface. DrTS shares high structural homology with sucrose hydrolase, amylosucrase and sucrose isomerase in complex with sucrose, in particular a virtually identical active-site architecture and a similar substrate-induced rotation of subdomain B. The inhibitor Tris was bound and mimics a sugar at the -1 subsite. A maltose was modelled into the active site, and subsequent mutational analysis suggested that Tyr213, Glu320 and Glu324 are essential within the +1 subsite for the TS activity. In addition, the interaction networks between subdomains B and S7 seal the active-site entrance. Disruption of such networks through the replacement of Arg148 and Asn253 with alanine resulted in a decrease in isomerase activity by 8-9-fold and an increased hydrolase activity by 1.5-1.8-fold. The N253A structure showed a small pore created for water entry. Therefore, our DrTS-Tris may represent a substrate-induced closed conformation that will facilitate intramolecular isomerization and minimize disaccharide hydrolysis.

-	~~The entry 4tvu~~ is ~~ON HOLD until Paper Publication~~	+	Structures of trehalose synthase from Deinococcus radiodurans reveal that a closed conformation is involved in catalysis of the intramolecular isomerization.,Wang YL, Chow SY, Lin YT, Hsieh YC, Lee GC, Liaw SH Acta Crystallogr D Biol Crystallogr. 2014 Dec 1;70(Pt 12):3144-54. doi:, 10.1107/S1399004714022500. Epub 2014 Nov 22. PMID:25478833<ref>PMID:25478833</ref>

-	~~Authors: Wang~~, Y.L., Chow, S.Y., Lin, Y.T., ~~Liaw, S.H.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of trehalose~~ synthase ~~from Deinococcus radiodurans reveals a closed conformation for catalysis of the intramolecular isomerization~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Maltose alpha-D-glucosyltransferase]]
		+	[[Category: Chow, S Y]]
		+	[[Category: Liaw, S H]]
		+	[[Category: Lin, Y T]]
		+	[[Category: Wang, Y L]]
		+	[[Category: Glycoside hydrolase family 13]]
		+	[[Category: Isomerase]]
		+	[[Category: Trehalose synthase]]
		+	[[Category: Tris complex]]

OCA at 08:32, 10 September 2014

2014-09-10T08:32:58Z

←Older revision		Revision as of 08:32, 10 September 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4tvu is ON HOLD	+	The entry 4tvu is ON HOLD until Paper Publication

-	Authors: Wang, Y.L., Lin, Y.T., Liaw, S.H.	+	Authors: Wang, Y.L., Chow, S.Y., Lin, Y.T., Liaw, S.H.

-	Description: Crystal structure of trehalose synthase from Deinococcus radiodurans reveals ~~an active~~ closed conformation	+	Description: Crystal structure of trehalose synthase from Deinococcus radiodurans reveals a closed conformation for catalysis of the intramolecular isomerization

OCA at 09:56, 16 July 2014

2014-07-16T09:56:16Z

←Older revision		Revision as of 09:56, 16 July 2014
Line 3:		Line 3:
	The entry 4tvu is ON HOLD		The entry 4tvu is ON HOLD

-	Authors: Wang, Y. L., Lin, Y. T., Liaw, S. H.	+	Authors: Wang, Y.L., Lin, Y.T., Liaw, S.H.

	Description: Crystal structure of trehalose synthase from Deinococcus radiodurans reveals an active closed conformation		Description: Crystal structure of trehalose synthase from Deinococcus radiodurans reveals an active closed conformation

OCA: Protected "4tvu" [edit=sysop:move=sysop]

2014-07-09T06:59:20Z

Protected "4tvu" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:59, 9 July 2014

OCA: New page: '''Unreleased structure''' The entry 4tvu is ON HOLD Authors: Wang, Y. L., Lin, Y. T., Liaw, S. H. Description: Crystal structure of trehalose synthase from Deinococcus radiodurans rev...

2014-07-09T06:59:18Z

New page: '''Unreleased structure''' The entry 4tvu is ON HOLD Authors: Wang, Y. L., Lin, Y. T., Liaw, S. H. Description: Crystal structure of trehalose synthase from Deinococcus radiodurans rev...

New page

'''Unreleased structure'''

The entry 4tvu is ON HOLD

Authors: Wang, Y. L., Lin, Y. T., Liaw, S. H.

Description: Crystal structure of trehalose synthase from Deinococcus radiodurans reveals an active closed conformation