2de2 - Revision history

OCA at 13:47, 13 March 2024

2024-03-13T13:47:21Z

←Older revision		Revision as of 13:47, 13 March 2024
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	<StructureSection load='2de2' size='340' side='right'caption='[[2de2]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2de2' size='340' side='right'caption='[[2de2]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Rhosg Rhosg~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DE2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp._IGTS8 Rhodococcus sp. IGTS8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DE2 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=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]] 1.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2de3\|2de3]], [[2de4\|2de4]]</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=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DSZB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~54064 RHOSG])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </~~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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [https://pdbe.org/2de2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [https://www.ebi.ac.uk/pdbsum/2de2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2de2 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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [https://pdbe.org/2de2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [https://www.ebi.ac.uk/pdbsum/2de2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2de2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~SOXB_RHOSG SOXB_RHOSG~~]~~] Part~~ of a pathway ~~to remove~~ covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. ~~This enzyme metabolizes DBT~~-~~sulfone~~ (~~DBTO2 or DBT 5,5~~-~~dioxide~~) to 2-hydroxybiphenyl (2-HBP).	+	[https://www.uniprot.org/uniprot/DSZB_RHOSG DSZB_RHOSG] Catalyzes the third and final step of the '4S' desulfurization pathway that removes covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. Oxidizes 2-(2'-hydroxyphenyl)benzene sulphinate (HBPS) to 2-hydroxybiphenyl (HBP) plus sulfite (PubMed:7961424, PubMed:7574582, PubMed:9634856, PubMed:9308179, PubMed:31545606). The rate-limiting step of the '4S' desulfurization pathway (PubMed:9308179, PubMed:31545606). The pathway substrate specificity has been augmented using mutagenesis, however no mutations allowed use of alkylated thiophenes (PubMed:11823208).<ref>PMID:11823208</ref> <ref>PMID:31545606</ref> <ref>PMID:7574582</ref> <ref>PMID:7961424</ref> <ref>PMID:9308179</ref> <ref>PMID:9634856</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=2de2 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=2de2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The desulfurization of dibenzothiophene in Rhodococcus erythropolis is catalyzed by two monooxygenases, DszA and DszC, and a desulfinase, DszB. In the last step of this pathway, DszB hydrolyzes 2'-hydroxybiphenyl-2-sulfinic acid into 2-hydroxybiphenyl and sulfite. We report on the crystal structures of DszB and an inactive mutant of DszB in complex with substrates at resolutions of 1.8A or better. The overall fold of DszB is similar to those of periplasmic substrate-binding proteins. In the substrate complexes, biphenyl rings of substrates are recognized by extensive hydrophobic interactions with the active site residues. Binding of substrates accompanies structural changes of the active site loops and recruits His(60) to the active site. The sulfinate group of bound substrates forms hydrogen bonds with side chains of Ser(27), His(60), and Arg(70), each of which is shown by site-directed mutagenesis to be essential for the activity. In our proposed reaction mechanism, Cys(27) functions as a nucleophile and seems to be activated by the sulfinate group of substrates, whereas His(60) and Arg(70) orient the syn orbital of sulfinate oxygen to the sulfhydryl hydrogen of Cys(27) and stabilize the negatively charged reaction intermediate. Cys, His, and Arg residues are conserved in putative proteins homologous to DszB, which are presumed to constitute a new family of desulfinases.
-
-	Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase.,Lee WC, Ohshiro T, Matsubara T, Izumi Y, Tanokura M J Biol Chem. 2006 Oct 27;281(43):32534-9. Epub 2006 Aug 4. PMID:16891315<ref>PMID:16891315</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2de2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Rhosg~~]]	+	[[Category: Rhodococcus sp. IGTS8]]
-	[[Category: Izumi, Y]]	+	[[Category: Izumi Y]]
-	[[Category: Lee~~, W C~~]]	+	[[Category: Lee WC]]
-	[[Category: Matsubara, T]]	+	[[Category: Matsubara T]]
-	[[Category: Ohshiro, T]]	+	[[Category: Ohshiro T]]
-	[[Category: Tanokura, M]]	+	[[Category: Tanokura M]]
-	~~[[Category: Alpha-beta]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 12:00, 3 February 2021

2021-02-03T12:00:57Z

←Older revision		Revision as of 12:00, 3 February 2021
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	==Crystal structure of desulfurization enzyme DSZB==		==Crystal structure of desulfurization enzyme DSZB==
-	<StructureSection load='2de2' size='340' side='right' caption='[[2de2]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2de2' size='340' side='right'caption='[[2de2]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Rhosg Rhosg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DE2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhosg Rhosg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DE2 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=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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2de3\|2de3]], [[2de4\|2de4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2de3\|2de3]], [[2de4\|2de4]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSZB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54064 RHOSG])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSZB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54064 RHOSG])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [~~http~~://pdbe.org/2de2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2de2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2de2 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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [https://pdbe.org/2de2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [https://www.ebi.ac.uk/pdbsum/2de2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2de2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SOXB_RHOSG SOXB_RHOSG]] Part of a pathway to remove covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. This enzyme metabolizes DBT-sulfone (DBTO2 or DBT 5,5-dioxide) to 2-hydroxybiphenyl (2-HBP).	+	[[https://www.uniprot.org/uniprot/SOXB_RHOSG SOXB_RHOSG]] Part of a pathway to remove covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. This enzyme metabolizes DBT-sulfone (DBTO2 or DBT 5,5-dioxide) to 2-hydroxybiphenyl (2-HBP).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]		[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]
		+	[[Category: Large Structures]]
	[[Category: Rhosg]]		[[Category: Rhosg]]
	[[Category: Izumi, Y]]		[[Category: Izumi, Y]]

OCA at 06:43, 30 May 2018

2018-05-30T06:43:40Z

←Older revision		Revision as of 06:43, 30 May 2018
Line 1:		Line 1:
		+
	==Crystal structure of desulfurization enzyme DSZB==		==Crystal structure of desulfurization enzyme DSZB==
	<StructureSection load='2de2' size='340' side='right' caption='[[2de2]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2de2' size='340' side='right' caption='[[2de2]], [[Resolution\|resolution]] 1.80Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSZB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54064 RHOSG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSZB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54064 RHOSG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [http://pdbe.org/2de2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [http://www.ebi.ac.uk/pdbsum/2de2 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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [http://pdbe.org/2de2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [http://www.ebi.ac.uk/pdbsum/2de2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2de2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/2de2_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/2de2_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2de2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:37, 11 September 2015

2015-09-11T11:37:17Z

←Older revision		Revision as of 11:37, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2de2' size='340' side='right' caption='[[2de2]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2de2' size='340' side='right' caption='[[2de2]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodococcus_sp. Rhodococcus sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DE2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhosg Rhosg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DE2 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=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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2de3\|2de3]], [[2de4\|2de4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2de3\|2de3]], [[2de4\|2de4]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSZB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1831 Rhodococcus sp.~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSZB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54064 RHOSG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [http://www.ebi.ac.uk/pdbsum/2de2 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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [http://pdbe.org/2de2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [http://www.ebi.ac.uk/pdbsum/2de2 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 2de2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]		[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]
-	[[Category: ~~Rhodococcus sp~~]]	+	[[Category: Rhosg]]
	[[Category: Izumi, Y]]		[[Category: Izumi, Y]]
	[[Category: Lee, W C]]		[[Category: Lee, W C]]

OCA at 15:56, 25 December 2014

2014-12-25T15:56:30Z

←Older revision		Revision as of 15:56, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DE2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DE2 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=GOL:GLYCEROL'>GOL</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=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2de3\|2de3]], [[2de4\|2de4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2de3\|2de3]], [[2de4\|2de4]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSZB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1831 Rhodococcus sp.])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSZB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1831 Rhodococcus sp.])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [http://www.ebi.ac.uk/pdbsum/2de2 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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [http://www.ebi.ac.uk/pdbsum/2de2 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SOXB_RHOSG SOXB_RHOSG]] Part of a pathway to remove covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. This enzyme metabolizes DBT-sulfone (DBTO2 or DBT 5,5-dioxide) to 2-hydroxybiphenyl (2-HBP).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]		[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]
-	[[Category: Rhodococcus sp.]]	+	[[Category: Rhodococcus sp]]
-	[[Category: Izumi, Y.]]	+	[[Category: Izumi, Y]]
-	[[Category: Lee, W C.]]	+	[[Category: Lee, W C]]
-	[[Category: Matsubara, T.]]	+	[[Category: Matsubara, T]]
-	[[Category: Ohshiro, T.]]	+	[[Category: Ohshiro, T]]
-	[[Category: Tanokura, M.]]	+	[[Category: Tanokura, M]]
	[[Category: Alpha-beta]]		[[Category: Alpha-beta]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 01:16, 30 September 2014

2014-09-30T01:16:58Z

←Older revision		Revision as of 01:16, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2de2.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of desulfurization enzyme DSZB==
		+	<StructureSection load='2de2' size='340' side='right' caption='[[2de2]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DE2 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=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2de3\|2de3]], [[2de4\|2de4]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DSZB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1831 Rhodococcus sp.])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [http://www.ebi.ac.uk/pdbsum/2de2 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/de/2de2_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 desulfurization of dibenzothiophene in Rhodococcus erythropolis is catalyzed by two monooxygenases, DszA and DszC, and a desulfinase, DszB. In the last step of this pathway, DszB hydrolyzes 2'-hydroxybiphenyl-2-sulfinic acid into 2-hydroxybiphenyl and sulfite. We report on the crystal structures of DszB and an inactive mutant of DszB in complex with substrates at resolutions of 1.8A or better. The overall fold of DszB is similar to those of periplasmic substrate-binding proteins. In the substrate complexes, biphenyl rings of substrates are recognized by extensive hydrophobic interactions with the active site residues. Binding of substrates accompanies structural changes of the active site loops and recruits His(60) to the active site. The sulfinate group of bound substrates forms hydrogen bonds with side chains of Ser(27), His(60), and Arg(70), each of which is shown by site-directed mutagenesis to be essential for the activity. In our proposed reaction mechanism, Cys(27) functions as a nucleophile and seems to be activated by the sulfinate group of substrates, whereas His(60) and Arg(70) orient the syn orbital of sulfinate oxygen to the sulfhydryl hydrogen of Cys(27) and stabilize the negatively charged reaction intermediate. Cys, His, and Arg residues are conserved in putative proteins homologous to DszB, which are presumed to constitute a new family of desulfinases.

-	~~{{STRUCTURE_2de2\| PDB=2de2 \| SCENE= }}~~	+	Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase.,Lee WC, Ohshiro T, Matsubara T, Izumi Y, Tanokura M J Biol Chem. 2006 Oct 27;281(43):32534-9. Epub 2006 Aug 4. PMID:16891315<ref>PMID:16891315</ref>

-	~~===Crystal structure~~ of ~~desulfurization enzyme DSZB===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16891315}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2de2]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodococcus_sp~~. ~~Rhodococcus sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016891315<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]		[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]
	[[Category: Rhodococcus sp.]]		[[Category: Rhodococcus sp.]]

OCA: Protected "2de2" [edit=sysop:move=sysop]

2013-01-06T10:31:27Z

Protected "2de2" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:31, 6 January 2013

OCA at 10:31, 6 January 2013

2013-01-06T10:31:24Z

←Older revision		Revision as of 10:31, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2de2.png\|left\|200px]]		[[Image:2de2.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2de2", 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_2de2\| PDB=2de2 \| SCENE= }}		{{STRUCTURE_2de2\| PDB=2de2 \| SCENE= }}

	===Crystal structure of desulfurization enzyme DSZB===		===Crystal structure of desulfurization enzyme DSZB===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16891315}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16891315 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16891315}}		{{ABSTRACT_PUBMED_16891315}}

	==About this Structure==		==About this Structure==
-	~~2DE2~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp.~~_igts8~~ Rhodococcus sp. ~~igts8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA].	+	[[2de2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16891315~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016891315</ref><references group="xtra"/>
	[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]		[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]
-	[[Category: Rhodococcus sp. ~~igts8~~]]	+	[[Category: Rhodococcus sp.]]
	[[Category: Izumi, Y.]]		[[Category: Izumi, Y.]]
	[[Category: Lee, W C.]]		[[Category: Lee, W C.]]
Line 33:		Line 21:
	[[Category: Alpha-beta]]		[[Category: Alpha-beta]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 11:23:15 2009''

OCA at 09:23, 22 March 2009

2009-03-22T09:23:15Z

←Older revision		Revision as of 09:23, 22 March 2009
Line 12:		Line 12:
	===Crystal structure of desulfurization enzyme DSZB===		===Crystal structure of desulfurization enzyme DSZB===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_16891315}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16891315 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16891315}}

	==About this Structure==		==About this Structure==
-	2DE2 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA].	+	2DE2 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp._igts8 Rhodococcus sp. igts8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:16891315</ref><references group="xtra"/>
	[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]		[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]
-	[[Category: Rhodococcus sp.]]	+	[[Category: Rhodococcus sp. igts8]]
	[[Category: Izumi, Y.]]		[[Category: Izumi, Y.]]
	[[Category: Lee, W C.]]		[[Category: Lee, W C.]]
Line 23:		Line 32:
	[[Category: Tanokura, M.]]		[[Category: Tanokura, M.]]
	[[Category: Alpha-beta]]		[[Category: Alpha-beta]]
		+	[[Category: Hydrolase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 21~~:03:59 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 11:23:15 2009''

OCA at 19:04, 17 February 2009

2009-02-17T19:04:01Z

←Older revision		Revision as of 19:04, 17 February 2009
Line 1:		Line 1:
-	[[Image:2de2.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2de2.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2de2\| PDB=2de2 \| SCENE= }}		{{STRUCTURE_2de2\| PDB=2de2 \| SCENE= }}

-	~~'''~~Crystal structure of desulfurization enzyme DSZB~~'''~~	+	===Crystal structure of desulfurization enzyme DSZB===


	==About this Structure==		==About this Structure==
-	2DE2 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA].	+	2DE2 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA].
	[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]		[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]
	[[Category: Rhodococcus sp.]]		[[Category: Rhodococcus sp.]]
-	[[Category: Single protein]]
	[[Category: Izumi, Y.]]		[[Category: Izumi, Y.]]
	[[Category: Lee, W C.]]		[[Category: Lee, W C.]]
Line 23:		Line 23:
	[[Category: Tanokura, M.]]		[[Category: Tanokura, M.]]
	[[Category: Alpha-beta]]		[[Category: Alpha-beta]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 00~~:15:~~08 2008~~''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:03:59 2009''