2qc5 - Revision history

OCA at 09:15, 21 February 2024

2024-02-21T09:15:13Z

←Older revision		Revision as of 09:15, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2qc5' size='340' side='right'caption='[[2qc5]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2qc5' size='340' side='right'caption='[[2qc5]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_29974 Atcc 29974~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~vgbB ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 ATCC 29974])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [https://pdbe.org/2qc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [https://www.ebi.ac.uk/pdbsum/2qc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qc5 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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [https://pdbe.org/2qc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [https://www.ebi.ac.uk/pdbsum/2qc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qc5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O87275_9STAP O87275_9STAP]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qc5 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=2qc5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The semisynthetic streptogramin antibiotic quinupristin/dalfopristin (trade name Synercid, Aventis Pharma) is a mixture of the A-type streptogramin dalfopristin and the B-type streptogramin quinupristin, a capped hexapeptide macrolactone. Quinupristin/dalfopristin was developed to combat multidrug resistant pathogens, but suffers from its own problems with drug resistance. Virginiamycin B lyase (Vgb) inactivates the quinupristin component of Synercid by lactone ring opening. Remarkably, the enzyme promotes this reaction by intramolecular beta-elimination without the involvement of a water molecule. Recently, structures of S. aureus Vgb in the presence and absence of substrate were reported and used together with detailed mutagenesis data to suggest a catalytic mechanism. Here, we report an independent determination of the S. cohnii Vgb crystal structure and a biochemical characterization of the enzyme. As expected, the S. cohnii and S. aureus Vgb structures and active sites are very similar. Moreover, both enzymes catalyze quinupristin lactone ring opening with similar rate constants, albeit perhaps with different dependencies on divalent metal ions. Replacement of the conserved active site residues His228, Glu268, or His270 with alanine reduces or abolishes S. cohnii Vgb activity. Residue Lys285 in S. cohnii Vgb is spatially equivalent to the S. aureus Vgb active site residue Glu284. A glutamate but not an alanine residue can substitute for the lysine without significant loss of activity.
-
-	Crystal structure and mechanism of the Staphylococcus cohnii virginiamycin B lyase (Vgb).,Lipka M, Filipek R, Bochtler M Biochemistry. 2008 Apr 8;47(14):4257-65. Epub 2008 Mar 15. PMID:18341294<ref>PMID:18341294</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2qc5" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 29974]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bochtler, M~~]]	+	[[Category: Staphylococcus cohnii]]
-	[[Category: ~~Lipka,~~ M]]	+	[[Category: Bochtler M]]
-	[[Category: ~~Beta propeller]]~~	+	[[Category: Lipka M]]
-	~~[[Category: Lyase~~]]	+

OCA at 08:15, 25 June 2021

2021-06-25T08:15:08Z

←Older revision		Revision as of 08:15, 25 June 2021
Line 1:		Line 1:

	==Streptogramin B lyase structure==		==Streptogramin B lyase structure==
-	<StructureSection load='2qc5' size='340' side='right' caption='[[2qc5]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2qc5' size='340' side='right'caption='[[2qc5]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_29974 Atcc 29974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_29974 Atcc 29974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vgbB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 ATCC 29974])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vgbB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 ATCC 29974])</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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [~~http~~://pdbe.org/2qc5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qc5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qc5 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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [https://pdbe.org/2qc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [https://www.ebi.ac.uk/pdbsum/2qc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qc5 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 29974]]		[[Category: Atcc 29974]]
		+	[[Category: Large Structures]]
	[[Category: Bochtler, M]]		[[Category: Bochtler, M]]
	[[Category: Lipka, M]]		[[Category: Lipka, M]]
	[[Category: Beta propeller]]		[[Category: Beta propeller]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 08:38, 29 August 2018

2018-08-29T08:38:26Z

←Older revision		Revision as of 08:38, 29 August 2018
Line 1:		Line 1:
		+
	==Streptogramin B lyase structure==		==Streptogramin B lyase structure==
	<StructureSection load='2qc5' size='340' side='right' caption='[[2qc5]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2qc5' size='340' side='right' caption='[[2qc5]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=IOD:IODIDE+ION'>IOD</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vgbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 ATCC 29974])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vgbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 ATCC 29974])</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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [http://pdbe.org/2qc5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [http://www.ebi.ac.uk/pdbsum/2qc5 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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [http://pdbe.org/2qc5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [http://www.ebi.ac.uk/pdbsum/2qc5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qc5 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qc/2qc5_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qc/2qc5_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 16:57, 7 February 2016

2016-02-07T16:57:46Z

←Older revision		Revision as of 16:57, 7 February 2016
Line 15:		Line 15:
	<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=2qc5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:26, 10 September 2015

2015-09-10T03:26:38Z

←Older revision		Revision as of 03:26, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2qc5' size='340' side='right' caption='[[2qc5]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2qc5' size='340' side='right' caption='[[2qc5]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_cohnii Staphylococcus cohnii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29974 Atcc 29974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vgbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 ~~Staphylococcus cohnii~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vgbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 ATCC 29974])</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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [http://www.ebi.ac.uk/pdbsum/2qc5 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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [http://pdbe.org/2qc5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [http://www.ebi.ac.uk/pdbsum/2qc5 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 2qc5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Staphylococcus cohnii~~]]	+	[[Category: Atcc 29974]]
	[[Category: Bochtler, M]]		[[Category: Bochtler, M]]
	[[Category: Lipka, M]]		[[Category: Lipka, M]]
	[[Category: Beta propeller]]		[[Category: Beta propeller]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 17:56, 19 January 2015

2015-01-19T17:56:28Z

←Older revision		Revision as of 17:56, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vgbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 Staphylococcus cohnii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vgbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 Staphylococcus cohnii])</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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [http://www.ebi.ac.uk/pdbsum/2qc5 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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [http://www.ebi.ac.uk/pdbsum/2qc5 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Staphylococcus cohnii]]		[[Category: Staphylococcus cohnii]]
-	[[Category: Bochtler, M.]]	+	[[Category: Bochtler, M]]
-	[[Category: Lipka, M.]]	+	[[Category: Lipka, M]]
	[[Category: Beta propeller]]		[[Category: Beta propeller]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 20:06, 30 September 2014

2014-09-30T20:06:30Z

←Older revision		Revision as of 20:06, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qc5.~~png~~\|~~left~~\|200px]]	+	==Streptogramin B lyase structure==
		+	<StructureSection load='2qc5' size='340' side='right' caption='[[2qc5]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vgbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 Staphylococcus cohnii])</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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [http://www.ebi.ac.uk/pdbsum/2qc5 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/qc/2qc5_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 semisynthetic streptogramin antibiotic quinupristin/dalfopristin (trade name Synercid, Aventis Pharma) is a mixture of the A-type streptogramin dalfopristin and the B-type streptogramin quinupristin, a capped hexapeptide macrolactone. Quinupristin/dalfopristin was developed to combat multidrug resistant pathogens, but suffers from its own problems with drug resistance. Virginiamycin B lyase (Vgb) inactivates the quinupristin component of Synercid by lactone ring opening. Remarkably, the enzyme promotes this reaction by intramolecular beta-elimination without the involvement of a water molecule. Recently, structures of S. aureus Vgb in the presence and absence of substrate were reported and used together with detailed mutagenesis data to suggest a catalytic mechanism. Here, we report an independent determination of the S. cohnii Vgb crystal structure and a biochemical characterization of the enzyme. As expected, the S. cohnii and S. aureus Vgb structures and active sites are very similar. Moreover, both enzymes catalyze quinupristin lactone ring opening with similar rate constants, albeit perhaps with different dependencies on divalent metal ions. Replacement of the conserved active site residues His228, Glu268, or His270 with alanine reduces or abolishes S. cohnii Vgb activity. Residue Lys285 in S. cohnii Vgb is spatially equivalent to the S. aureus Vgb active site residue Glu284. A glutamate but not an alanine residue can substitute for the lysine without significant loss of activity.

-	~~{{STRUCTURE_2qc5\| PDB=2qc5 \| SCENE= }}~~	+	Crystal structure and mechanism of the Staphylococcus cohnii virginiamycin B lyase (Vgb).,Lipka M, Filipek R, Bochtler M Biochemistry. 2008 Apr 8;47(14):4257-65. Epub 2008 Mar 15. PMID:18341294<ref>PMID:18341294</ref>

-	~~===Streptogramin B lyase structure===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18341294}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2qc5]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018341294<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Staphylococcus cohnii]]		[[Category: Staphylococcus cohnii]]
	[[Category: Bochtler, M.]]		[[Category: Bochtler, M.]]

OCA: Protected "2qc5" [edit=sysop:move=sysop]

2013-01-07T22:59:24Z

Protected "2qc5" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:59, 7 January 2013

OCA at 22:59, 7 January 2013

2013-01-07T22:59:22Z

←Older revision		Revision as of 22:59, 7 January 2013
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-	{{Seed}}
	[[Image:2qc5.png\|left\|200px]]		[[Image:2qc5.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qc5", 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_2qc5\| PDB=2qc5 \| SCENE= }}		{{STRUCTURE_2qc5\| PDB=2qc5 \| SCENE= }}

	===Streptogramin B lyase structure===		===Streptogramin B lyase structure===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18341294}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18341294 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18341294}}		{{ABSTRACT_PUBMED_18341294}}

	==About this Structure==		==About this Structure==
-	~~2QC5~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA].	+	[[2qc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18341294~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018341294</ref><references group="xtra"/>
	[[Category: Staphylococcus cohnii]]		[[Category: Staphylococcus cohnii]]
	[[Category: Bochtler, M.]]		[[Category: Bochtler, M.]]
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	[[Category: Beta propeller]]		[[Category: Beta propeller]]
	[[Category: Lyase]]		[[Category: Lyase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:16:45 2009''

OCA at 13:16, 16 February 2009

2009-02-16T13:16:46Z

←Older revision		Revision as of 13:16, 16 February 2009
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	{{Seed}}		{{Seed}}
-	[[Image:2qc5.~~jpg~~\|left\|200px]]	+	[[Image:2qc5.png\|left\|200px]]

	<!--		<!--
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	==About this Structure==		==About this Structure==
-	2QC5 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA].	+	2QC5 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA].

	==Reference==		==Reference==
-	~~Crystal structure and mechanism of the Staphylococcus cohnii virginiamycin B lyase (Vgb)., Lipka M, Filipek R, Bochtler M, Biochemistry. 2008 Apr 8;47(14):4257-65. Epub 2008 Mar 15.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18341294 18341294]~~	+	<ref group="xtra">PMID:18341294</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Staphylococcus cohnii]]		[[Category: Staphylococcus cohnii]]
	[[Category: Bochtler, M.]]		[[Category: Bochtler, M.]]
Line 31:		Line 30:
	[[Category: Lyase]]		[[Category: Lyase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Oct~~ 15 14:09:~~32 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:16:45 2009''