2rez - Revision history

OCA at 11:55, 30 August 2023

2023-08-30T11:55:14Z

←Older revision		Revision as of 11:55, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2rez' size='340' side='right'caption='[[2rez]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2rez' size='340' side='right'caption='[[2rez]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rez]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"actinomyces_glaucescens"_preobrazhenskaya_in_gauze_et_al._1957 "actinomyces~~ glaucescens~~" preobrazhenskaya in gauze et al. 1957~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2REZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rez]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_glaucescens Streptomyces glaucescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2REZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 1.95Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2rer\|2rer]], [[2res\|2res]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">tcmN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 "Actinomyces glaucescens" Preobrazhenskaya in Gauze et al. 1957])~~</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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [https://pdbe.org/2rez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [https://www.ebi.ac.uk/pdbsum/2rez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rez 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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [https://pdbe.org/2rez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [https://www.ebi.ac.uk/pdbsum/2rez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rez ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TCMN_STRGA TCMN_STRGA]] The N-terminal domain enhances the formation of an early, partially cyclized intermediate, while the C-terminal domain catalyzes the 3-O-methylation of one or more later intermediates in the biosynthetic pathway. Catalyzes the methylation of tetracenomycin D3 (Tcm D3) to yield Tcm B3. Catalyzes as well the following side reactions: methylation of 8-O-methyl-Tcm D3 to yield Tcm E; and of 9-carboxymethyl-Tcm B3 to yield Tcm A2.	+	[https://www.uniprot.org/uniprot/TCMN_STRGA TCMN_STRGA] The N-terminal domain enhances the formation of an early, partially cyclized intermediate, while the C-terminal domain catalyzes the 3-O-methylation of one or more later intermediates in the biosynthetic pathway. Catalyzes the methylation of tetracenomycin D3 (Tcm D3) to yield Tcm B3. Catalyzes as well the following side reactions: methylation of 8-O-methyl-Tcm D3 to yield Tcm E; and of 9-carboxymethyl-Tcm B3 to yield Tcm A2.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Actinomyces glaucescens preobrazhenskaya in gauze et al. 1957]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ames, B D~~]]	+	[[Category: Streptomyces glaucescens]]
-	[[Category: ~~Tsai, S C~~]]	+	[[Category: Ames BD]]
-	[[Category: ~~Antibiotic biosynthesis]]~~	+	[[Category: Tsai SC]]
-	~~[[Category: Aromatase]]~~	+
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Cyclase]]~~	+
-	~~[[Category: Dehydratase]]~~	+
-	~~[[Category: Double-hot-dog]]~~	+
-	~~[[Category: Helix-grip]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Multifunctional enzyme]]~~	+
-	~~[[Category: Polyketide]]~~	+
-	~~[[Category: Tetracenomycin]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 04:23, 2 July 2021

2021-07-02T04:23:24Z

←Older revision		Revision as of 04:23, 2 July 2021
Line 1:		Line 1:

	==Tetracenomycin ARO/CYC NaI Structure==		==Tetracenomycin ARO/CYC NaI Structure==
-	<StructureSection load='2rez' size='340' side='right' caption='[[2rez]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='2rez' size='340' side='right'caption='[[2rez]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rez]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"actinomyces_glaucescens"_preobrazhenskaya_in_gauze_et_al._1957 "actinomyces glaucescens" preobrazhenskaya in gauze et al. 1957]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2REZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rez]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_glaucescens"_preobrazhenskaya_in_gauze_et_al._1957 "actinomyces glaucescens" preobrazhenskaya in gauze et al. 1957]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2REZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rer\|2rer]], [[2res\|2res]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2rer\|2rer]], [[2res\|2res]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tcmN ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 "Actinomyces glaucescens" Preobrazhenskaya in Gauze et al. 1957])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tcmN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 "Actinomyces glaucescens" Preobrazhenskaya in Gauze et al. 1957])</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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [~~http~~://pdbe.org/2rez PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rez PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rez 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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [https://pdbe.org/2rez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [https://www.ebi.ac.uk/pdbsum/2rez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rez ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TCMN_STRGA TCMN_STRGA]] The N-terminal domain enhances the formation of an early, partially cyclized intermediate, while the C-terminal domain catalyzes the 3-O-methylation of one or more later intermediates in the biosynthetic pathway. Catalyzes the methylation of tetracenomycin D3 (Tcm D3) to yield Tcm B3. Catalyzes as well the following side reactions: methylation of 8-O-methyl-Tcm D3 to yield Tcm E; and of 9-carboxymethyl-Tcm B3 to yield Tcm A2.	+	[[https://www.uniprot.org/uniprot/TCMN_STRGA TCMN_STRGA]] The N-terminal domain enhances the formation of an early, partially cyclized intermediate, while the C-terminal domain catalyzes the 3-O-methylation of one or more later intermediates in the biosynthetic pathway. Catalyzes the methylation of tetracenomycin D3 (Tcm D3) to yield Tcm B3. Catalyzes as well the following side reactions: methylation of 8-O-methyl-Tcm D3 to yield Tcm E; and of 9-carboxymethyl-Tcm B3 to yield Tcm A2.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Actinomyces glaucescens preobrazhenskaya in gauze et al. 1957]]		[[Category: Actinomyces glaucescens preobrazhenskaya in gauze et al. 1957]]
		+	[[Category: Large Structures]]
	[[Category: Ames, B D]]		[[Category: Ames, B D]]
	[[Category: Tsai, S C]]		[[Category: Tsai, S C]]

OCA at 11:13, 5 September 2018

2018-09-05T11:13:04Z

←Older revision		Revision as of 11:13, 5 September 2018
Line 1:		Line 1:
		+
	==Tetracenomycin ARO/CYC NaI Structure==		==Tetracenomycin ARO/CYC NaI Structure==
	<StructureSection load='2rez' size='340' side='right' caption='[[2rez]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2rez' size='340' side='right' caption='[[2rez]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rer\|2rer]], [[2res\|2res]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rer\|2rer]], [[2res\|2res]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tcmN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 "Actinomyces glaucescens" Preobrazhenskaya in Gauze et al. 1957])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tcmN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 "Actinomyces glaucescens" Preobrazhenskaya in Gauze et al. 1957])</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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [http://pdbe.org/2rez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [http://www.ebi.ac.uk/pdbsum/2rez 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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [http://pdbe.org/2rez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [http://www.ebi.ac.uk/pdbsum/2rez PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rez ProSAT]</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/re/2rez_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/2rez_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 07:08, 7 February 2016

2016-02-07T07:08:34Z

←Older revision		Revision as of 07:08, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='2rez' size='340' side='right' caption='[[2rez]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2rez' size='340' side='right' caption='[[2rez]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rez]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_glaucescens Streptomyces~~ glaucescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2REZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rez]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_glaucescens"_preobrazhenskaya_in_gauze_et_al._1957 "actinomyces glaucescens" preobrazhenskaya in gauze et al. 1957]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2REZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rer\|2rer]], [[2res\|2res]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rer\|2rer]], [[2res\|2res]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tcmN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 ~~Streptomyces~~ glaucescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tcmN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 "Actinomyces glaucescens" Preobrazhenskaya in Gauze et al. 1957])</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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [http://www.ebi.ac.uk/pdbsum/2rez 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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [http://pdbe.org/2rez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [http://www.ebi.ac.uk/pdbsum/2rez PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=2rez ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 2rez" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptomyces~~ glaucescens]]	+	[[Category: Actinomyces glaucescens preobrazhenskaya in gauze et al. 1957]]
	[[Category: Ames, B D]]		[[Category: Ames, B D]]
	[[Category: Tsai, S C]]		[[Category: Tsai, S C]]

OCA at 08:52, 24 December 2014

2014-12-24T08:52:26Z

←Older revision		Revision as of 08:52, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rez]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_glaucescens Streptomyces glaucescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2REZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rez]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_glaucescens Streptomyces glaucescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2REZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rer\|2rer]], [[2res\|2res]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rer\|2rer]], [[2res\|2res]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tcmN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 Streptomyces glaucescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tcmN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 Streptomyces glaucescens])</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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [http://www.ebi.ac.uk/pdbsum/2rez 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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [http://www.ebi.ac.uk/pdbsum/2rez PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TCMN_STRGA TCMN_STRGA]] The N-terminal domain enhances the formation of an early, partially cyclized intermediate, while the C-terminal domain catalyzes the 3-O-methylation of one or more later intermediates in the biosynthetic pathway. Catalyzes the methylation of tetracenomycin D3 (Tcm D3) to yield Tcm B3. Catalyzes as well the following side reactions: methylation of 8-O-methyl-Tcm D3 to yield Tcm E; and of 9-carboxymethyl-Tcm B3 to yield Tcm A2.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Streptomyces glaucescens]]		[[Category: Streptomyces glaucescens]]
-	[[Category: Ames, B D.]]	+	[[Category: Ames, B D]]
-	[[Category: Tsai, S C.]]	+	[[Category: Tsai, S C]]
	[[Category: Antibiotic biosynthesis]]		[[Category: Antibiotic biosynthesis]]
	[[Category: Aromatase]]		[[Category: Aromatase]]

OCA at 19:29, 30 September 2014

2014-09-30T19:29:09Z

←Older revision		Revision as of 19:29, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2rez.~~png~~\|~~left~~\|200px]]	+	==Tetracenomycin ARO/CYC NaI Structure==
		+	<StructureSection load='2rez' size='340' side='right' caption='[[2rez]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rez]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_glaucescens Streptomyces glaucescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2REZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rer\|2rer]], [[2res\|2res]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tcmN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1907 Streptomyces glaucescens])</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=2rez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rez OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rez RCSB], [http://www.ebi.ac.uk/pdbsum/2rez 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/re/2rez_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 ==
		+	Polyketides are a class of natural products with highly diverse chemical structures and pharmaceutical activities. Polyketide cyclization, promoted by the aromatase/cyclase (ARO/CYC), helps diversify aromatic polyketides. How the ARO/CYC promotes highly specific cyclization is not well understood because of the lack of a first-ring ARO/CYC structure. The 1.9 A crystal structure of Tcm ARO/CYC reveals that the enzyme belongs to the Bet v1-like superfamily (or STAR domain family) with a helix-grip fold, and contains a highly conserved interior pocket. Docking, mutagenesis, and an in vivo assay show that the size, shape, and composition of the pocket are important to orient and specifically fold the polyketide chain for C9-C14 first-ring and C7-C16 second-ring cyclizations. Two pocket residues, R69 and Y35, were found to be essential for promoting first- and second-ring cyclization specificity. Different pocket residue mutations affected the polyketide product distribution. A mechanism is proposed based on the structure-mutation-docking results. These results strongly suggest that the regiospecific cyclizations of the first two rings and subsequent aromatizations take place in the interior pocket. The chemical insights gleaned from this work pave the foundation toward defining the molecular rules for the ARO/CYC cyclization specificity, whose rational control will be important for future endeavors in the engineered biosynthesis of novel anticancer and antibiotic aromatic polyketides.

-	~~{{STRUCTURE_2rez\| PDB=2rez \| SCENE= }}~~	+	Crystal structure and functional analysis of tetracenomycin ARO/CYC: implications for cyclization specificity of aromatic polyketides.,Ames BD, Korman TP, Zhang W, Smith P, Vu T, Tang Y, Tsai SC Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5349-54. Epub 2008 Apr 3. PMID:18388203<ref>PMID:18388203</ref>

-	~~===Tetracenomycin ARO~~/~~CYC NaI Structure===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18388203}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2rez]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptomyces_glaucescens Streptomyces glaucescens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018388203<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Streptomyces glaucescens]]		[[Category: Streptomyces glaucescens]]
	[[Category: Ames, B D.]]		[[Category: Ames, B D.]]

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

2013-01-07T19:33:53Z

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

←Older revision

Revision as of 19:33, 7 January 2013

OCA at 19:33, 7 January 2013

2013-01-07T19:33:51Z

←Older revision		Revision as of 19:33, 7 January 2013
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-	{{Seed}}
	[[Image:2rez.png\|left\|200px]]		[[Image:2rez.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rez", 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_2rez\| PDB=2rez \| SCENE= }}		{{STRUCTURE_2rez\| PDB=2rez \| SCENE= }}

	===Tetracenomycin ARO/CYC NaI Structure===		===Tetracenomycin ARO/CYC NaI Structure===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18388203}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18388203 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18388203}}		{{ABSTRACT_PUBMED_18388203}}

	==About this Structure==		==About this Structure==
-	~~2REZ~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_glaucescens Streptomyces glaucescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA].	+	[[2rez]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_glaucescens Streptomyces glaucescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18388203~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018388203</ref><references group="xtra"/>
	[[Category: Streptomyces glaucescens]]		[[Category: Streptomyces glaucescens]]
	[[Category: Ames, B D.]]		[[Category: Ames, B D.]]
Line 39:		Line 27:
	[[Category: Tetracenomycin]]		[[Category: Tetracenomycin]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:10:10 2009''

OCA at 10:10, 16 February 2009

2009-02-16T10:10:10Z

←Older revision		Revision as of 10:10, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2REZ is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_glaucescens Streptomyces glaucescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA].	+	2REZ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_glaucescens Streptomyces glaucescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2REZ OCA].

	==Reference==		==Reference==
-	Crystal structure and functional analysis of tetracenomycin ARO/CYC: implications for cyclization specificity of aromatic polyketides., Ames BD, Korman TP, Zhang W, Smith P, Vu T, Tang Y, Tsai SC, Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5349-54. Epub 2008 Apr 3. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18388203 18388203]~~	+	<ref group="xtra">PMID:18388203</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Streptomyces glaucescens]]		[[Category: Streptomyces glaucescens]]
	[[Category: Ames, B D.]]		[[Category: Ames, B D.]]
Line 41:		Line 40:
	[[Category: Transferase]]		[[Category: Transferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 14~~:20:~~43 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:10:10 2009''

OCA at 11:20, 27 July 2008

2008-07-27T11:20:49Z

←Older revision		Revision as of 11:20, 27 July 2008
Line 1:		Line 1:
-	[[Image:2rez.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2rez.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2rez\| PDB=2rez \| SCENE= }}		{{STRUCTURE_2rez\| PDB=2rez \| SCENE= }}

-	~~'''~~Tetracenomycin ARO/CYC NaI Structure~~'''~~	+	===Tetracenomycin ARO/CYC NaI Structure===


-	~~==Overview==~~	+	<!--
-	~~Polyketides are a class of natural products with highly diverse chemical structures and pharmaceutical activities. Polyketide cyclization~~, ~~promoted by~~ the ~~aromatase/cyclase~~ (~~ARO~~/~~CYC), helps diversify aromatic polyketides. How the ARO~~/~~CYC promotes highly specific cyclization is not well understood because of the lack of a first-ring ARO/CYC structure~~. ~~The 1~~.~~9 A crystal structure of Tcm ARO/CYC reveals that the enzyme belongs to the Bet v1-like superfamily (or STAR domain family~~) ~~with a helix-grip fold~~, ~~and contains a highly conserved interior pocket. Docking, mutagenesis, and an in vivo assay show that~~ the ~~size, shape, and composition of the pocket are important to orient and specifically fold the polyketide chain for C9-C14 first-ring and C7-C16 second-ring cyclizations~~. ~~Two pocket residues, R69 and Y35, were found to be essential for promoting first~~- ~~and second~~-ring cyclization specificity. Different pocket residue mutations affected the polyketide product distribution. A mechanism is proposed based on the structure-mutation-docking results. These results strongly suggest that the regiospecific cyclizations of the first two rings and subsequent aromatizations take place in the interior pocket. The chemical insights gleaned from this work pave the foundation toward defining the molecular rules for the ARO/CYC cyclization specificity, whose rational control will be important for future endeavors in the engineered biosynthesis of novel anticancer and antibiotic aromatic polyketides.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18388203}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18388203 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18388203}}

	==About this Structure==		==About this Structure==
Line 36:		Line 40:
	[[Category: Tetracenomycin]]		[[Category: Tetracenomycin]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Apr 24 09~~:42:23 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 14:20:43 2008''