2dzw - Revision history

OCA at 08:32, 25 October 2023

OCA — Wed, 25 Oct 2023 08:32:46 GMT

←Older revision		Revision as of 08:32, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2dzw' size='340' side='right'caption='[[2dzw]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2dzw' size='340' side='right'caption='[[2dzw]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dzw]] 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=2DZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dzw]] 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=2DZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DZW 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]], [[2dzu\|2dzu]], [[2dzv\|2dzv]], [[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]] 2.4Å</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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [https://pdbe.org/2dzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [https://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzw ProSAT], [https://www.topsan.org/Proteins/RSGI/2dzw 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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [https://pdbe.org/2dzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [https://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzw ProSAT], [https://www.topsan.org/Proteins/RSGI/2dzw 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=2dzw 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=2dzw 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 2dzw" 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

OCA — Wed, 10 Feb 2021 11:43:33 GMT

←Older revision		Revision as of 11:43, 10 February 2021
Line 1:		Line 1:

	==Structure of mutant tryptophan synthase alpha-subunit (E244A) from a hyperthermophile, Pyrococcus furiosus==		==Structure of mutant tryptophan synthase alpha-subunit (E244A) from a hyperthermophile, Pyrococcus furiosus==
-	<StructureSection load='2dzw' size='340' side='right' caption='[[2dzw]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='2dzw' size='340' side='right'caption='[[2dzw]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dzw]] 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=2DZW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dzw]] 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=2DZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DZW 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]], [[2dzu\|2dzu]], [[2dzv\|2dzv]], [[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]], [[2dzu\|2dzu]], [[2dzv\|2dzv]], [[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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [~~http~~://pdbe.org/2dzw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzw ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2dzw 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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [https://pdbe.org/2dzw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [https://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzw ProSAT], [https://www.topsan.org/Proteins/RSGI/2dzw 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 07:10, 6 June 2018

OCA — Wed, 06 Jun 2018 07:10:18 GMT

←Older revision		Revision as of 07:10, 6 June 2018
Line 1:		Line 1:
		+
	==Structure of mutant tryptophan synthase alpha-subunit (E244A) from a hyperthermophile, Pyrococcus furiosus==		==Structure of mutant tryptophan synthase alpha-subunit (E244A) from a hyperthermophile, Pyrococcus furiosus==
	<StructureSection load='2dzw' size='340' side='right' caption='[[2dzw]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2dzw' size='340' side='right' caption='[[2dzw]], [[Resolution\|resolution]] 2.40Å' 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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [http://pdbe.org/2dzw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [http://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzw 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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [http://pdbe.org/2dzw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [http://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dzw ProSAT], [http://www.topsan.org/Proteins/RSGI/2dzw 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/2dzw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dz/2dzw_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 11:45, 7 February 2016

OCA — Sun, 07 Feb 2016 11:45:31 GMT

←Older revision		Revision as of 11:45, 7 February 2016
Line 18:		Line 18:
	<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=2dzw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:11, 10 September 2015

OCA — Thu, 10 Sep 2015 01:11:07 GMT

←Older revision		Revision as of 01:11, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2dzw' size='340' side='right' caption='[[2dzw]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2dzw' size='340' side='right' caption='[[2dzw]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dzw]] 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=2DZW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dzw]] 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=2DZW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZW 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]], [[2dzu\|2dzu]], [[2dzv\|2dzv]], [[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]], [[2dzu\|2dzu]], [[2dzv\|2dzv]], [[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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [http://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzw 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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [http://pdbe.org/2dzw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [http://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzw 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 2dzw" 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 14:50, 24 December 2014

OCA — Wed, 24 Dec 2014 14:50:29 GMT

←Older revision		Revision as of 14:50, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dzw]] 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=2DZW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZW FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dzw]] 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=2DZW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZW 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]], [[2dzu\|2dzu]], [[2dzv\|2dzv]], [[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]], [[2dzu\|2dzu]], [[2dzv\|2dzv]], [[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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [http://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzw 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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [http://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzw 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 00:30, 30 September 2014

OCA — Tue, 30 Sep 2014 00:30:03 GMT

←Older revision		Revision as of 00:30, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2dzw.~~png~~\|~~left~~\|200px]]	+	==Structure of mutant tryptophan synthase alpha-subunit (E244A) from a hyperthermophile, Pyrococcus furiosus==
		+	<StructureSection load='2dzw' size='340' side='right' caption='[[2dzw]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dzw]] 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=2DZW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DZW 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]], [[2dzu\|2dzu]], [[2dzv\|2dzv]], [[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=2dzw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dzw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dzw RCSB], [http://www.ebi.ac.uk/pdbsum/2dzw PDBsum], [http://www.topsan.org/Proteins/RSGI/2dzw 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/2dzw_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_2dzw\| PDB=2dzw \| 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 (E244A) 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 ==
-	[[~~2dzw~~]] 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=2DZW 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 "2dzw" [edit=sysop:move=sysop]

OCA — Sun, 06 Jan 2013 09:52:26 GMT

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

←Older revision

Revision as of 09:52, 6 January 2013

OCA at 09:52, 6 January 2013

OCA — Sun, 06 Jan 2013 09:52:23 GMT

←Older revision		Revision as of 09:52, 6 January 2013
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-	{{Seed}}
	[[Image:2dzw.png\|left\|200px]]		[[Image:2dzw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2dzw", 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_2dzw\| PDB=2dzw \| SCENE= }}		{{STRUCTURE_2dzw\| PDB=2dzw \| SCENE= }}

	===Structure of mutant tryptophan synthase alpha-subunit (E244A) from a hyperthermophile, Pyrococcus furiosus===		===Structure of mutant tryptophan synthase alpha-subunit (E244A) from a hyperthermophile, Pyrococcus furiosus===

		+	{{ABSTRACT_PUBMED_11118452}}

	==About this Structure==		==About this Structure==
-	~~2DZW~~ 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=2DZW OCA].	+	[[2dzw]] 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=2DZW 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 Mon Feb 16 13:34:53 2009''

OCA at 11:34, 16 February 2009

OCA — Mon, 16 Feb 2009 11:34:56 GMT

←Older revision		Revision as of 11:34, 16 February 2009
Line 12:		Line 12:
	===Structure of mutant tryptophan synthase alpha-subunit (E244A) from a hyperthermophile, Pyrococcus furiosus===		===Structure of mutant tryptophan synthase alpha-subunit (E244A) 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 15:40:~~38 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:34:53 2009''