2rdr - Revision history

OCA at 09:21, 21 February 2024

2024-02-21T09:21:42Z

←Older revision		Revision as of 09:21, 21 February 2024
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	<StructureSection load='2rdr' size='340' side='right'caption='[[2rdr]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2rdr' size='340' side='right'caption='[[2rdr]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rdr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"streptomyces_avermitilis"_burg_et_al._1979 "streptomyces~~ avermitilis~~" burg et al. 1979~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rdr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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]] 1.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ptlH ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])~~</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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [https://pdbe.org/2rdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [https://www.ebi.ac.uk/pdbsum/2rdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdr 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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [https://pdbe.org/2rdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [https://www.ebi.ac.uk/pdbsum/2rdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PTLH_STRAW PTLH_STRAW]] Catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:16704250</ref> <ref>PMID:17942405</ref>	+	[https://www.uniprot.org/uniprot/PTLH_STRAW PTLH_STRAW] Catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:16704250</ref> <ref>PMID:17942405</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2rdr 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=2rdr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The non-heme iron dioxygenase PtlH from the soil organism Streptomyces avermitilis is a member of the iron(II)/alpha-ketoglutarate-dependent dioxygenase superfamily and catalyzes an essential reaction in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone. To investigate the structural basis for substrate recognition and catalysis, we have determined the x-ray crystal structure of PtlH in several complexes with the cofactors iron, alpha-ketoglutarate, and the non-reactive enantiomer of the substrate, ent-1-deoxypentalenic acid, in four different crystal forms to up to 1.31 A resolution. The overall structure of PtlH forms a double-stranded barrel helix fold, and the cofactor-binding site for iron and alpha-ketoglutarate is similar to other double-stranded barrel helix fold enzymes. Additional secondary structure elements that contribute to the substrate-binding site in PtlH are not conserved in other double-stranded barrel helix fold enzymes. Binding of the substrate enantiomer induces a reorganization of the monoclinic crystal lattice leading to a disorder-order transition of a C-terminal alpha-helix. The newly formed helix blocks the major access to the active site and effectively traps the bound substrate. Kinetic analysis of wild type and site-directed mutant proteins confirms a critical function of two arginine residues in substrate binding, while simulated docking of the enzymatic reaction product reveals the likely orientation of bound substrate.
-
-	Crystal structure of the non-heme iron dioxygenase PtlH in pentalenolactone biosynthesis.,You Z, Omura S, Ikeda H, Cane DE, Jogl G J Biol Chem. 2007 Dec 14;282(50):36552-60. Epub 2007 Oct 16. PMID:17942405<ref>PMID:17942405</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2rdr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Streptomyces avermitilis burg et al. 1979]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cane~~, D E~~]]	+	[[Category: Streptomyces avermitilis]]
-	[[Category: Ikeda, H]]	+	[[Category: Cane DE]]
-	[[Category: Jogl, G]]	+	[[Category: Ikeda H]]
-	[[Category: Omura, S]]	+	[[Category: Jogl G]]
-	[[Category: You, Z]]	+	[[Category: Omura S]]
-	~~[[Category: Dioxygenase]]~~	+	[[Category: You Z]]
-	~~[[Category: Double stranded barrel helix]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 04:22, 2 July 2021

2021-07-02T04:22:30Z

←Older revision		Revision as of 04:22, 2 July 2021
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	==Crystal Structure of PtlH with Fe/oxalylglycine bound==		==Crystal Structure of PtlH with Fe/oxalylglycine bound==
-	<StructureSection load='2rdr' size='340' side='right' caption='[[2rdr]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='2rdr' size='340' side='right'caption='[[2rdr]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rdr]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"streptomyces_avermitilis"_burg_et_al._1979 "streptomyces avermitilis" burg et al. 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rdr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"streptomyces_avermitilis"_burg_et_al._1979 "streptomyces avermitilis" burg et al. 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptlH ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptlH ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [~~http~~://pdbe.org/2rdr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rdr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdr 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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [https://pdbe.org/2rdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [https://www.ebi.ac.uk/pdbsum/2rdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PTLH_STRAW PTLH_STRAW]] Catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:16704250</ref> <ref>PMID:17942405</ref>	+	[[https://www.uniprot.org/uniprot/PTLH_STRAW PTLH_STRAW]] Catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:16704250</ref> <ref>PMID:17942405</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rdr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rdr_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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Streptomyces avermitilis burg et al. 1979]]		[[Category: Streptomyces avermitilis burg et al. 1979]]
		+	[[Category: Large Structures]]
	[[Category: Cane, D E]]		[[Category: Cane, D E]]
	[[Category: Ikeda, H]]		[[Category: Ikeda, H]]

OCA at 07:49, 25 October 2017

2017-10-25T07:49:30Z

←Older revision		Revision as of 07:49, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of PtlH with Fe/oxalylglycine bound==		==Crystal Structure of PtlH with Fe/oxalylglycine bound==
	<StructureSection load='2rdr' size='340' side='right' caption='[[2rdr]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2rdr' size='340' side='right' caption='[[2rdr]], [[Resolution\|resolution]] 1.70Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [http://pdbe.org/2rdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [http://www.ebi.ac.uk/pdbsum/2rdr 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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [http://pdbe.org/2rdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [http://www.ebi.ac.uk/pdbsum/2rdr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:29, 7 February 2016

2016-02-07T07:29:23Z

←Older revision		Revision as of 07:29, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='2rdr' size='340' side='right' caption='[[2rdr]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2rdr' size='340' side='right' caption='[[2rdr]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_avermitilis Streptomyces~~ avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_avermitilis"_burg_et_al._1979 "streptomyces avermitilis" burg et al. 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [http://www.ebi.ac.uk/pdbsum/2rdr 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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [http://pdbe.org/2rdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [http://www.ebi.ac.uk/pdbsum/2rdr PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~Q82IZ1_STRAW Q82IZ1_STRAW~~]] Catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:16704250</ref> <ref>PMID:17942405</ref>	+	[[http://www.uniprot.org/uniprot/PTLH_STRAW PTLH_STRAW]] Catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:16704250</ref> <ref>PMID:17942405</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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=2rdr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 2rdr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Streptomyces avermitilis]]	+	[[Category: Streptomyces avermitilis burg et al. 1979]]
	[[Category: Cane, D E]]		[[Category: Cane, D E]]
	[[Category: Ikeda, H]]		[[Category: Ikeda, H]]

OCA at 08:59, 24 December 2014

2014-12-24T08:59:40Z

←Older revision		Revision as of 08:59, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [http://www.ebi.ac.uk/pdbsum/2rdr 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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [http://www.ebi.ac.uk/pdbsum/2rdr PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q82IZ1_STRAW Q82IZ1_STRAW]] Catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:16704250</ref> <ref>PMID:17942405</ref>
	== 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 avermitilis]]		[[Category: Streptomyces avermitilis]]
-	[[Category: Cane, D E.]]	+	[[Category: Cane, D E]]
-	[[Category: Ikeda, H.]]	+	[[Category: Ikeda, H]]
-	[[Category: Jogl, G.]]	+	[[Category: Jogl, G]]
-	[[Category: Omura, S.]]	+	[[Category: Omura, S]]
-	[[Category: You, Z.]]	+	[[Category: You, Z]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]
	[[Category: Double stranded barrel helix]]		[[Category: Double stranded barrel helix]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 19:34, 30 September 2014

2014-09-30T19:34:17Z

←Older revision		Revision as of 19:34, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2rdr.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of PtlH with Fe/oxalylglycine bound==
		+	<StructureSection load='2rdr' size='340' side='right' caption='[[2rdr]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rdn\|2rdn]], [[2rdq\|2rdq]], [[2rds\|2rds]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptlH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</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=2rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rdr RCSB], [http://www.ebi.ac.uk/pdbsum/2rdr 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/rd/2rdr_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 non-heme iron dioxygenase PtlH from the soil organism Streptomyces avermitilis is a member of the iron(II)/alpha-ketoglutarate-dependent dioxygenase superfamily and catalyzes an essential reaction in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone. To investigate the structural basis for substrate recognition and catalysis, we have determined the x-ray crystal structure of PtlH in several complexes with the cofactors iron, alpha-ketoglutarate, and the non-reactive enantiomer of the substrate, ent-1-deoxypentalenic acid, in four different crystal forms to up to 1.31 A resolution. The overall structure of PtlH forms a double-stranded barrel helix fold, and the cofactor-binding site for iron and alpha-ketoglutarate is similar to other double-stranded barrel helix fold enzymes. Additional secondary structure elements that contribute to the substrate-binding site in PtlH are not conserved in other double-stranded barrel helix fold enzymes. Binding of the substrate enantiomer induces a reorganization of the monoclinic crystal lattice leading to a disorder-order transition of a C-terminal alpha-helix. The newly formed helix blocks the major access to the active site and effectively traps the bound substrate. Kinetic analysis of wild type and site-directed mutant proteins confirms a critical function of two arginine residues in substrate binding, while simulated docking of the enzymatic reaction product reveals the likely orientation of bound substrate.

-	~~{{STRUCTURE_2rdr\| PDB=2rdr \| SCENE= }}~~	+	Crystal structure of the non-heme iron dioxygenase PtlH in pentalenolactone biosynthesis.,You Z, Omura S, Ikeda H, Cane DE, Jogl G J Biol Chem. 2007 Dec 14;282(50):36552-60. Epub 2007 Oct 16. PMID:17942405<ref>PMID:17942405</ref>

-	~~===Crystal Structure of PtlH with Fe~~/~~oxalylglycine bound===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17942405}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2rdr]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2RDR OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017942405<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Streptomyces avermitilis]]		[[Category: Streptomyces avermitilis]]
	[[Category: Cane, D E.]]		[[Category: Cane, D E.]]

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

2013-01-07T19:40:36Z

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

←Older revision

Revision as of 19:40, 7 January 2013

OCA at 19:40, 7 January 2013

2013-01-07T19:40:34Z

←Older revision		Revision as of 19:40, 7 January 2013
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-	{{Seed}}
	[[Image:2rdr.png\|left\|200px]]		[[Image:2rdr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rdr", 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_2rdr\| PDB=2rdr \| SCENE= }}		{{STRUCTURE_2rdr\| PDB=2rdr \| SCENE= }}

	===Crystal Structure of PtlH with Fe/oxalylglycine bound===		===Crystal Structure of PtlH with Fe/oxalylglycine bound===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17942405}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17942405 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17942405}}		{{ABSTRACT_PUBMED_17942405}}

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

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17942405~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017942405</ref><references group="xtra"/>
	[[Category: Streptomyces avermitilis]]		[[Category: Streptomyces avermitilis]]
	[[Category: Cane, D E.]]		[[Category: Cane, D E.]]
Line 33:		Line 21:
	[[Category: Double stranded barrel helix]]		[[Category: Double stranded barrel helix]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:16:16 2009''

OCA at 10:16, 16 February 2009

2009-02-16T10:16:17Z

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

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

	==Reference==		==Reference==
-	~~Crystal structure of the non-heme iron dioxygenase PtlH in pentalenolactone biosynthesis., You Z, Omura S, Ikeda H, Cane DE, Jogl G, J Biol Chem. 2007 Dec 14;282(50):36552-60. Epub 2007 Oct 16.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17942405 17942405]~~	+	<ref group="xtra">PMID:17942405</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Streptomyces avermitilis]]		[[Category: Streptomyces avermitilis]]
	[[Category: Cane, D E.]]		[[Category: Cane, D E.]]
Line 35:		Line 34:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 14~~:27:~~38 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:16:16 2009''

OCA at 11:27, 27 July 2008

2008-07-27T11:27:41Z

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

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2rdr\| PDB=2rdr \| SCENE= }}		{{STRUCTURE_2rdr\| PDB=2rdr \| SCENE= }}

-	~~'''~~Crystal Structure of PtlH with Fe/oxalylglycine bound~~'''~~	+	===Crystal Structure of PtlH with Fe/oxalylglycine bound===


-	~~==Overview==~~	+	<!--
-	The ~~non-heme iron dioxygenase PtlH from~~ the ~~soil organism Streptomyces avermitilis is a member of~~ the ~~iron~~(~~II)~~/~~alpha-ketoglutarate-dependent dioxygenase superfamily and catalyzes an essential reaction in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone~~. To investigate the structural basis for substrate recognition and catalysis, we have determined the x-ray crystal structure of PtlH in several complexes with the cofactors iron, alpha-ketoglutarate, and the non-reactive enantiomer of the substrate, ent-1-deoxypentalenic acid, in four different crystal forms to up to 1.~~31 A resolution. The overall structure of PtlH forms a double-stranded barrel helix fold~~, ~~and the cofactor-binding site for iron and alpha-ketoglutarate~~ is ~~similar to other double-stranded barrel helix fold enzymes. Additional secondary structure elements that contribute to~~ the ~~substrate-binding site in PtlH are not conserved in other double-stranded barrel helix fold enzymes~~. ~~Binding of the substrate enantiomer induces a reorganization of the monoclinic crystal lattice leading to a disorder~~-~~order transition of a C~~-terminal alpha-helix. The newly formed helix blocks the major access to the active site and effectively traps the bound substrate. Kinetic analysis of wild type and site-directed mutant proteins confirms a critical function of two arginine residues in substrate binding, while simulated docking of the enzymatic reaction product reveals the likely orientation of bound substrate.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17942405}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17942405 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17942405}}

	==About this Structure==		==About this Structure==
Line 30:		Line 34:
	[[Category: Double stranded barrel helix]]		[[Category: Double stranded barrel helix]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun ~~May 4 16:42~~:27 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 14:27:38 2008''