2dzu - Revision history

OCA at 08:32, 25 October 2023

2023-10-25T08:32:43Z

←Older revision		Revision as of 08:32, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2dzu' size='340' side='right'caption='[[2dzu]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='2dzu' size='340' side='right'caption='[[2dzu]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dzu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43587 Atcc 43587~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dzu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DZU FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1geq\|1geq]], [[2dzp\|2dzp]], [[2dzs\|2dzs]], [[2dzt\|2dzt]], [[2dzv\|2dzv]], [[2dzw\|2dzw]], [[2dzx\|2dzx]]</div></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]] 2.46Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">trpA ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=2261 ATCC 43587])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [https://pdbe.org/2dzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [https://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzu ProSAT], [https://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [https://pdbe.org/2dzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [https://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzu ProSAT], [https://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TRPA_PYRFU TRPA_PYRFU]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate.	+	[https://www.uniprot.org/uniprot/TRPA_PYRFU TRPA_PYRFU] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 19:
	</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=2dzu 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=2dzu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of the tryptophan synthase alpha-subunit from Pyrococcus furiosus was determined by x-ray analysis at 2.0-A resolution, and its stability was examined by differential scanning calorimetry. Although the structure of the tryptophan synthase alpha(2)beta(2) complex from Salmonella typhimurium has been already determined, this is the first report of the structure of the alpha-subunit alone. The alpha-subunit from P. furiosus (Pf-alpha-subunit) lacked 12 and 6 residues at the N and C termini, respectively, and one residue each in two loop regions as compared with that from S. typhimurium (St-alpha-subunit), resulting in the absence of an N-terminal helix and the shortening of a C-terminal helix. The structure of the Pf-alpha-subunit was essentially similar to that of the St-alpha-subunit in the alpha(2)beta(2) complex. The differences between both structures were discussed in connection with the higher stability of the Pf-alpha-subunit and the complex formation of the alpha- and beta-subunits. Calorimetric results indicated that the Pf-alpha-subunit has extremely high thermostability and that its higher stability is caused by an entropic effect. On the basis of structural information of both proteins, we analyzed the contributions of each stabilization factor and could conclude that hydrophobic interactions in the protein interior do not contribute to the higher stability of the Pf-alpha-subunit. Rather, the increase in ion pairs, decrease in cavity volume, and entropic effects due to shortening of the polypeptide chain play important roles in extremely high stability in Pf-alpha-subunit.
-
-	Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry.,Yamagata Y, Ogasahara K, Hioki Y, Lee SJ, Nakagawa A, Nakamura H, Ishida M, Kuramitsu S, Yutani K J Biol Chem. 2001 Apr 6;276(14):11062-71. Epub 2000 Dec 15. PMID:11118452<ref>PMID:11118452</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2dzu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Tryptophan synthase 3D structures\|Tryptophan synthase 3D structures]]		*[[Tryptophan synthase 3D structures\|Tryptophan synthase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43587]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Tryptophan synthase]]
-	[[Category: Ogasahara, K]]
-	[[Category: Structural genomic]]
-	[[Category: Yamagata, Y]]
-	[[Category: Yutani, K]]
-	[[Category: Calorimetry]]
-	[[Category: Hyperthermophile]]
-	[[Category: Lyase]]
-	[[Category: National project on protein structural and functional analyse]]
-	[[Category: Nppsfa]]
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
-	[[Category: ~~Rsgi~~]]	+	[[Category: Ogasahara K]]
-	[[Category: ~~Stability~~]]	+	[[Category: Yamagata Y]]
-	[[Category: ~~Tryptophan synthase alpha-subunit]]~~	+	[[Category: Yutani K]]
-	~~[[Category: X-ray analysis~~]]	+

OCA at 11:43, 10 February 2021

2021-02-10T11:43:17Z

←Older revision		Revision as of 11:43, 10 February 2021
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	==Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile, Pyrococcus furiosus==		==Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile, Pyrococcus furiosus==
-	<StructureSection load='2dzu' size='340' side='right' caption='[[2dzu]], [[Resolution\|resolution]] 2.46Å' scene=''>	+	<StructureSection load='2dzu' size='340' side='right'caption='[[2dzu]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dzu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dzu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DZU FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1geq\|1geq]], [[2dzp\|2dzp]], [[2dzs\|2dzs]], [[2dzt\|2dzt]], [[2dzv\|2dzv]], [[2dzw\|2dzw]], [[2dzx\|2dzx]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1geq\|1geq]], [[2dzp\|2dzp]], [[2dzs\|2dzs]], [[2dzt\|2dzt]], [[2dzv\|2dzv]], [[2dzw\|2dzw]], [[2dzx\|2dzx]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [~~http~~://pdbe.org/2dzu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzu ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [https://pdbe.org/2dzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [https://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzu ProSAT], [https://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TRPA_PYRFU TRPA_PYRFU]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate.	+	[[https://www.uniprot.org/uniprot/TRPA_PYRFU TRPA_PYRFU]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Tryptophan synthase\|Tryptophan synthase]]	+	*[[Tryptophan synthase 3D structures\|Tryptophan synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43587]]		[[Category: Atcc 43587]]
		+	[[Category: Large Structures]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
	[[Category: Ogasahara, K]]		[[Category: Ogasahara, K]]

OCA at 06:54, 6 June 2018

2018-06-06T06:54:41Z

←Older revision		Revision as of 06:54, 6 June 2018
Line 1:		Line 1:
		+
	==Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile, Pyrococcus furiosus==		==Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile, Pyrococcus furiosus==
	<StructureSection load='2dzu' size='340' side='right' caption='[[2dzu]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='2dzu' size='340' side='right' caption='[[2dzu]], [[Resolution\|resolution]] 2.46Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [http://pdbe.org/2dzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [http://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [http://pdbe.org/2dzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [http://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzu ProSAT], [http://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dz/2dzu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dz/2dzu_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>
	</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=2dzu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:21, 11 September 2015

2015-09-11T15:21:35Z

←Older revision		Revision as of 15:21, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2dzu' size='340' side='right' caption='[[2dzu]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='2dzu' size='340' side='right' caption='[[2dzu]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dzu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_furiosus Pyrococcus furiosus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dzu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZU FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1geq\|1geq]], [[2dzp\|2dzp]], [[2dzs\|2dzs]], [[2dzt\|2dzt]], [[2dzv\|2dzv]], [[2dzw\|2dzw]], [[2dzx\|2dzx]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1geq\|1geq]], [[2dzp\|2dzp]], [[2dzs\|2dzs]], [[2dzt\|2dzt]], [[2dzv\|2dzv]], [[2dzw\|2dzw]], [[2dzx\|2dzx]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ~~Pyrococcus furiosus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [http://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [http://pdbe.org/2dzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [http://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2dzu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus furiosus~~]]	+	[[Category: Atcc 43587]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
	[[Category: Ogasahara, K]]		[[Category: Ogasahara, K]]
Line 46:		Line 47:
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
		+	[[Category: Pyrococcus furiosus]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Stability]]		[[Category: Stability]]
	[[Category: Tryptophan synthase alpha-subunit]]		[[Category: Tryptophan synthase alpha-subunit]]
	[[Category: X-ray analysis]]		[[Category: X-ray analysis]]

OCA at 18:19, 25 December 2014

2014-12-25T18:19:34Z

←Older revision		Revision as of 18:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dzu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZU FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dzu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1geq\|1geq]], [[2dzp\|2dzp]], [[2dzs\|2dzs]], [[2dzt\|2dzt]], [[2dzv\|2dzv]], [[2dzw\|2dzw]], [[2dzx\|2dzx]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1geq\|1geq]], [[2dzp\|2dzp]], [[2dzs\|2dzs]], [[2dzt\|2dzt]], [[2dzv\|2dzv]], [[2dzw\|2dzw]], [[2dzx\|2dzx]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [http://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [http://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TRPA_PYRFU TRPA_PYRFU]] The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
-	[[Category: Ogasahara, K.]]	+	[[Category: Ogasahara, K]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Yamagata, Y.]]	+	[[Category: Yamagata, Y]]
-	[[Category: Yutani, K.]]	+	[[Category: Yutani, K]]
	[[Category: Calorimetry]]		[[Category: Calorimetry]]
	[[Category: Hyperthermophile]]		[[Category: Hyperthermophile]]
Line 44:		Line 46:
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
-	[[Category: Pyrococcus furiosus]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Stability]]		[[Category: Stability]]
-	[[Category: Structural genomic]]
	[[Category: Tryptophan synthase alpha-subunit]]		[[Category: Tryptophan synthase alpha-subunit]]
	[[Category: X-ray analysis]]		[[Category: X-ray analysis]]

OCA at 01:55, 30 September 2014

2014-09-30T01:55:29Z

←Older revision		Revision as of 01:55, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2dzu.~~png~~\|~~left~~\|200px]]	+	==Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile, Pyrococcus furiosus==
		+	<StructureSection load='2dzu' size='340' side='right' caption='[[2dzu]], [[Resolution\|resolution]] 2.46Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dzu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1geq\|1geq]], [[2dzp\|2dzp]], [[2dzs\|2dzs]], [[2dzt\|2dzt]], [[2dzv\|2dzv]], [[2dzw\|2dzw]], [[2dzx\|2dzx]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan_synthase Tryptophan synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.20 4.2.1.20] </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=2dzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dzu RCSB], [http://www.ebi.ac.uk/pdbsum/2dzu PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzu TOPSAN]</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/dz/2dzu_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 structure of the tryptophan synthase alpha-subunit from Pyrococcus furiosus was determined by x-ray analysis at 2.0-A resolution, and its stability was examined by differential scanning calorimetry. Although the structure of the tryptophan synthase alpha(2)beta(2) complex from Salmonella typhimurium has been already determined, this is the first report of the structure of the alpha-subunit alone. The alpha-subunit from P. furiosus (Pf-alpha-subunit) lacked 12 and 6 residues at the N and C termini, respectively, and one residue each in two loop regions as compared with that from S. typhimurium (St-alpha-subunit), resulting in the absence of an N-terminal helix and the shortening of a C-terminal helix. The structure of the Pf-alpha-subunit was essentially similar to that of the St-alpha-subunit in the alpha(2)beta(2) complex. The differences between both structures were discussed in connection with the higher stability of the Pf-alpha-subunit and the complex formation of the alpha- and beta-subunits. Calorimetric results indicated that the Pf-alpha-subunit has extremely high thermostability and that its higher stability is caused by an entropic effect. On the basis of structural information of both proteins, we analyzed the contributions of each stabilization factor and could conclude that hydrophobic interactions in the protein interior do not contribute to the higher stability of the Pf-alpha-subunit. Rather, the increase in ion pairs, decrease in cavity volume, and entropic effects due to shortening of the polypeptide chain play important roles in extremely high stability in Pf-alpha-subunit.

-	~~{{STRUCTURE_2dzu\| PDB=2dzu \| SCENE= }}~~	+	Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry.,Yamagata Y, Ogasahara K, Hioki Y, Lee SJ, Nakagawa A, Nakamura H, Ishida M, Kuramitsu S, Yutani K J Biol Chem. 2001 Apr 6;276(14):11062-71. Epub 2000 Dec 15. PMID:11118452<ref>PMID:11118452</ref>

-	~~===Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile~~, ~~Pyrococcus furiosus===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_11118452}}~~	+	==See Also==
-		+	*[[Tryptophan synthase\|Tryptophan synthase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2dzu~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:011118452<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]

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

2013-01-06T11:08:48Z

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

←Older revision

Revision as of 11:08, 6 January 2013

OCA at 11:08, 6 January 2013

2013-01-06T11:08:46Z

←Older revision		Revision as of 11:08, 6 January 2013
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-	{{Seed}}
	[[Image:2dzu.png\|left\|200px]]		[[Image:2dzu.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2dzu", 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_2dzu\| PDB=2dzu \| SCENE= }}		{{STRUCTURE_2dzu\| PDB=2dzu \| SCENE= }}

	===Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile, Pyrococcus furiosus===		===Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile, Pyrococcus furiosus===

		+	{{ABSTRACT_PUBMED_11118452}}

	==About this Structure==		==About this Structure==
-	~~2DZU~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA].	+	[[2dzu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11118452~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011118452</ref><references group="xtra"/>
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
Line 36:		Line 30:
	[[Category: Tryptophan synthase alpha-subunit]]		[[Category: Tryptophan synthase alpha-subunit]]
	[[Category: X-ray analysis]]		[[Category: X-ray analysis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:58:16 2009''

OCA at 23:58, 17 February 2009

2009-02-17T23:58:19Z

←Older revision		Revision as of 23:58, 17 February 2009
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	===Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile, Pyrococcus furiosus===		===Structure of mutant tryptophan synthase alpha-subunit (D110N) from a hyperthermophile, Pyrococcus furiosus===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11118452}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11118452 is the PubMed ID number.
-	-->
-	{{ABSTRACT_PUBMED_11118452}}

	==About this Structure==		==About this Structure==
Line 23:		Line 17:

	==Reference==		==Reference==
-	Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry., Yamagata Y, Ogasahara K, Hioki Y, Lee SJ, Nakagawa A, Nakamura H, Ishida M, Kuramitsu S, Yutani K, J Biol Chem. 2001 Apr 6;276(14):11062-71. Epub 2000 Dec 15. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/11118452 11118452]~~	+	<ref group="xtra">PMID:11118452</ref><references group="xtra"/>
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
Line 43:		Line 37:
	[[Category: X-ray analysis]]		[[Category: X-ray analysis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 17~~:22:~~10 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:58:16 2009''

OCA at 15:22, 16 November 2008

2008-11-16T15:22:14Z

←Older revision		Revision as of 15:22, 16 November 2008
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	==About this Structure==		==About this Structure==
-	2DZU is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA].	+	2DZU is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DZU OCA].

	==Reference==		==Reference==
	Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry., Yamagata Y, Ogasahara K, Hioki Y, Lee SJ, Nakagawa A, Nakamura H, Ishida M, Kuramitsu S, Yutani K, J Biol Chem. 2001 Apr 6;276(14):11062-71. Epub 2000 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11118452 11118452]		Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry., Yamagata Y, Ogasahara K, Hioki Y, Lee SJ, Nakagawa A, Nakamura H, Ishida M, Kuramitsu S, Yutani K, J Biol Chem. 2001 Apr 6;276(14):11062-71. Epub 2000 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11118452 11118452]
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
-	[[Category: Single protein]]
	[[Category: Tryptophan synthase]]		[[Category: Tryptophan synthase]]
	[[Category: Ogasahara, K.]]		[[Category: Ogasahara, K.]]
Line 44:		Line 43:
	[[Category: X-ray analysis]]		[[Category: X-ray analysis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Sep 29 04~~:57:31 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 17:22:10 2008''