3d8s - Revision history

OCA at 09:40, 21 February 2024

OCA — Wed, 21 Feb 2024 09:40:20 GMT

←Older revision		Revision as of 09:40, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3d8s' size='340' side='right'caption='[[3d8s]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3d8s' size='340' side='right'caption='[[3d8s]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d8s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thet2 Thet2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d8s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D8S FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1jr2\|1jr2]]~~, [[~~1wd7~~\|~~1wd7~~]]~~, [[3d8n\|3d8n]], [[3d8r\|3d8r]], [[3d8t\|3d8t]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>TT_C0312 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~262724 THET2])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Uroporphyrinogen-III_synthase Uroporphyrinogen-III synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.75 4.2.1.75]~~ </~~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=3d8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8s OCA], [https://pdbe.org/3d8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d8s RCSB], [https://www.ebi.ac.uk/pdbsum/3d8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8s 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=3d8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8s OCA], [https://pdbe.org/3d8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d8s RCSB], [https://www.ebi.ac.uk/pdbsum/3d8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8s ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q72KM1_THET2 Q72KM1_THET2]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3d8s 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=3d8s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Uroporphyrinogen III synthase (U3S) catalyzes the asymmetrical cyclization of a linear tetrapyrrole to form the physiologically relevant uroporphyrinogen III (uro'gen III) isomer during heme biosynthesis. Here, we report four apoenzyme and one product complex crystal structures of the Thermus thermophilus (HB27) U3S protein. The overlay of eight crystallographically unique U3S molecules reveals a huge range of conformational flexibility, including a "closed" product complex. The product, uro'gen III, binds between the two domains and is held in place by a network of hydrogen bonds between the product's side chain carboxylates and the protein's main chain amides. Interactions of the product A and B ring carboxylate side chains with both structural domains of U3S appear to dictate the relative orientation of the domains in the closed enzyme conformation and likely remain intact during catalysis. The product C and D rings are less constrained in the structure, consistent with the conformational changes required for the catalytic cyclization with inversion of D ring orientation. A conserved tyrosine residue is potentially positioned to facilitate loss of a hydroxyl from the substrate to initiate the catalytic reaction.
-
-	Structure and Mechanistic Implications of a Uroporphyrinogen III Synthase-Product Complex.,Schubert HL, Phillips JD, Heroux A, Hill CP Biochemistry. 2008 Jul 24. PMID:18651750<ref>PMID:18651750</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3d8s" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet2]]~~	+	[[Category: Thermus thermophilus HB27]]
-	~~[[Category: Uroporphyrinogen-III synthase~~]]	+	[[Category: Schubert HL]]
-	[[Category: Schubert~~, H L]]~~	+
-	~~[[Category: Heme biosynthesis]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 07:56, 2 February 2022

OCA — Wed, 02 Feb 2022 07:56:58 GMT

←Older revision		Revision as of 07:56, 2 February 2022
Line 1:		Line 1:

	==Thermus thermophilus Uroporphyrinogen III Synthase==		==Thermus thermophilus Uroporphyrinogen III Synthase==
-	<StructureSection load='3d8s' size='340' side='right' caption='[[3d8s]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3d8s' size='340' side='right'caption='[[3d8s]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d8s]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3D8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d8s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D8S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jr2\|1jr2]], [[1wd7\|1wd7]], [[3d8n\|3d8n]], [[3d8r\|3d8r]], [[3d8t\|3d8t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jr2\|1jr2]], [[1wd7\|1wd7]], [[3d8n\|3d8n]], [[3d8r\|3d8r]], [[3d8t\|3d8t]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0312 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0312 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Uroporphyrinogen-III_synthase Uroporphyrinogen-III synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.75 4.2.1.75] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uroporphyrinogen-III_synthase Uroporphyrinogen-III synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.75 4.2.1.75] </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=3d8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8s OCA], [~~http~~://pdbe.org/3d8s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3d8s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3d8s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8s 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=3d8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8s OCA], [https://pdbe.org/3d8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d8s RCSB], [https://www.ebi.ac.uk/pdbsum/3d8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8s ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d8/3d8s_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d8/3d8s_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>
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thet2]]		[[Category: Thet2]]
	[[Category: Uroporphyrinogen-III synthase]]		[[Category: Uroporphyrinogen-III synthase]]

OCA at 08:44, 25 October 2017

OCA — Wed, 25 Oct 2017 08:44:11 GMT

←Older revision		Revision as of 08:44, 25 October 2017
Line 1:		Line 1:
		+
	==Thermus thermophilus Uroporphyrinogen III Synthase==		==Thermus thermophilus Uroporphyrinogen III Synthase==
	<StructureSection load='3d8s' size='340' side='right' caption='[[3d8s]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3d8s' size='340' side='right' caption='[[3d8s]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0312 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0312 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen-III_synthase Uroporphyrinogen-III synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.75 4.2.1.75] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen-III_synthase Uroporphyrinogen-III synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.75 4.2.1.75] </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=3d8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8s OCA], [http://pdbe.org/3d8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d8s RCSB], [http://www.ebi.ac.uk/pdbsum/3d8s 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=3d8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8s OCA], [http://pdbe.org/3d8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d8s RCSB], [http://www.ebi.ac.uk/pdbsum/3d8s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8s ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 01:45, 9 February 2016

OCA — Tue, 09 Feb 2016 01:45:36 GMT

←Older revision		Revision as of 01:45, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3d8s' size='340' side='right' caption='[[3d8s]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3d8s' size='340' side='right' caption='[[3d8s]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3d8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3d8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jr2\|1jr2]], [[1wd7\|1wd7]], [[3d8n\|3d8n]], [[3d8r\|3d8r]], [[3d8t\|3d8t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jr2\|1jr2]], [[1wd7\|1wd7]], [[3d8n\|3d8n]], [[3d8r\|3d8r]], [[3d8t\|3d8t]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0312 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~274 Thermus thermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0312 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen-III_synthase Uroporphyrinogen-III synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.75 4.2.1.75] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen-III_synthase Uroporphyrinogen-III synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.75 4.2.1.75] </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=3d8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d8s RCSB], [http://www.ebi.ac.uk/pdbsum/3d8s 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=3d8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8s OCA], [http://pdbe.org/3d8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d8s RCSB], [http://www.ebi.ac.uk/pdbsum/3d8s PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3d8s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3d8s" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Thet2]]
	[[Category: Uroporphyrinogen-III synthase]]		[[Category: Uroporphyrinogen-III synthase]]
	[[Category: Schubert, H L]]		[[Category: Schubert, H L]]
	[[Category: Heme biosynthesis]]		[[Category: Heme biosynthesis]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 08:12, 12 November 2014

OCA — Wed, 12 Nov 2014 08:12:14 GMT

←Older revision		Revision as of 08:12, 12 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3d8s.~~png~~\|~~left~~\|200px]]	+	==Thermus thermophilus Uroporphyrinogen III Synthase==
		+	<StructureSection load='3d8s' size='340' side='right' caption='[[3d8s]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3d8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8S FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jr2\|1jr2]], [[1wd7\|1wd7]], [[3d8n\|3d8n]], [[3d8r\|3d8r]], [[3d8t\|3d8t]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0312 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen-III_synthase Uroporphyrinogen-III synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.75 4.2.1.75] </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=3d8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d8s RCSB], [http://www.ebi.ac.uk/pdbsum/3d8s PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d8/3d8s_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 ==
		+	Uroporphyrinogen III synthase (U3S) catalyzes the asymmetrical cyclization of a linear tetrapyrrole to form the physiologically relevant uroporphyrinogen III (uro'gen III) isomer during heme biosynthesis. Here, we report four apoenzyme and one product complex crystal structures of the Thermus thermophilus (HB27) U3S protein. The overlay of eight crystallographically unique U3S molecules reveals a huge range of conformational flexibility, including a "closed" product complex. The product, uro'gen III, binds between the two domains and is held in place by a network of hydrogen bonds between the product's side chain carboxylates and the protein's main chain amides. Interactions of the product A and B ring carboxylate side chains with both structural domains of U3S appear to dictate the relative orientation of the domains in the closed enzyme conformation and likely remain intact during catalysis. The product C and D rings are less constrained in the structure, consistent with the conformational changes required for the catalytic cyclization with inversion of D ring orientation. A conserved tyrosine residue is potentially positioned to facilitate loss of a hydroxyl from the substrate to initiate the catalytic reaction.

-	~~{{STRUCTURE_3d8s\| PDB=3d8s \| SCENE= }}~~	+	Structure and Mechanistic Implications of a Uroporphyrinogen III Synthase-Product Complex.,Schubert HL, Phillips JD, Heroux A, Hill CP Biochemistry. 2008 Jul 24. PMID:18651750<ref>PMID:18651750</ref>

-	~~===Thermus thermophilus Uroporphyrinogen III Synthase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18651750}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3d8s]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018651750<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Uroporphyrinogen-III synthase]]		[[Category: Uroporphyrinogen-III synthase]]
-	[[Category: Schubert, H L.]]	+	[[Category: Schubert, H L]]
	[[Category: Heme biosynthesis]]		[[Category: Heme biosynthesis]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA: Protected "3d8s" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 19:01:05 GMT

Protected "3d8s" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:01, 7 January 2013

OCA at 19:00, 7 January 2013

OCA — Mon, 07 Jan 2013 19:00:59 GMT

←Older revision		Revision as of 19:00, 7 January 2013
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-	{{Seed}}
	[[Image:3d8s.png\|left\|200px]]		[[Image:3d8s.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3d8s", 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_3d8s\| PDB=3d8s \| SCENE= }}		{{STRUCTURE_3d8s\| PDB=3d8s \| SCENE= }}

	===Thermus thermophilus Uroporphyrinogen III Synthase===		===Thermus thermophilus Uroporphyrinogen III Synthase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18651750}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18651750 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18651750}}		{{ABSTRACT_PUBMED_18651750}}

	==About this Structure==		==About this Structure==
-	~~3D8S~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA].	+	[[3d8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18651750~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018651750</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Uroporphyrinogen-III synthase]]		[[Category: Uroporphyrinogen-III synthase]]
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	[[Category: Heme biosynthesis]]		[[Category: Heme biosynthesis]]
	[[Category: Lyase]]		[[Category: Lyase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:27:33 2009''

OCA at 03:27, 17 February 2009

OCA — Tue, 17 Feb 2009 03:27:34 GMT

←Older revision		Revision as of 03:27, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3D8S is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA].	+	3D8S is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA].

	==Reference==		==Reference==
-	~~Structure and Mechanistic Implications of a Uroporphyrinogen III Synthase-Product Complex., Schubert HL, Phillips JD, Heroux A, Hill CP, Biochemistry. 2008 Jul 24.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18651750 18651750]~~	+	<ref group="xtra">PMID:18651750</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Uroporphyrinogen-III synthase]]		[[Category: Uroporphyrinogen-III synthase]]
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	[[Category: Lyase]]		[[Category: Lyase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Aug 27 10~~:34:~~24 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:27:33 2009''

OCA at 07:34, 27 August 2008

OCA — Wed, 27 Aug 2008 07:34:25 GMT

←Older revision		Revision as of 07:34, 27 August 2008
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3d8s.~~jpg~~\|left\|200px]]	+	[[Image:3d8s.png\|left\|200px]]

	<!--		<!--
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	[[Category: Lyase]]		[[Category: Lyase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug ~~6 13~~:02:45 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 27 10:34:24 2008''

OCA at 10:02, 6 August 2008

OCA — Wed, 06 Aug 2008 10:02:46 GMT

←Older revision		Revision as of 10:02, 6 August 2008
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3d8s.jpg\|left\|200px]]

-	The ~~entry 3d8s~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3d8s", 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_3d8s\| PDB=3d8s \| SCENE= }}

-	~~Authors: Schubert, H.L.~~	+	===Thermus thermophilus Uroporphyrinogen III Synthase===

-	Description: Thermus thermophilus Uroporphyrinogen III Synthase

		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18651750}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18651750 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18651750}}

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 11 09~~:38:14 2008''	+	==About this Structure==
		+	3D8S is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8S OCA].
		+
		+	==Reference==
		+	Structure and Mechanistic Implications of a Uroporphyrinogen III Synthase-Product Complex., Schubert HL, Phillips JD, Heroux A, Hill CP, Biochemistry. 2008 Jul 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18651750 18651750]
		+	[[Category: Single protein]]
		+	[[Category: Thermus thermophilus]]
		+	[[Category: Uroporphyrinogen-III synthase]]
		+	[[Category: Schubert, H L.]]
		+	[[Category: Heme biosynthesis]]
		+	[[Category: Lyase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 6 13:02:45 2008''