1pyy - Revision history

OCA at 09:53, 16 August 2023

OCA — Wed, 16 Aug 2023 09:53:04 GMT

←Older revision		Revision as of 09:53, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1pyy' size='340' side='right'caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='1pyy' size='340' side='right'caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Strr6 Strr6~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PYY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GLC:ALPHA~~-~~D-GLUCOSE'>GLC</scene>~~, ~~<scene name='pdbligand=MPD:(4S)-~~2~~-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.42Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~TRV~~:'>~~TRV~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PRD_900045:octanoyl-sucrose,+esterificated+at+fructose+C6'>PRD_900045</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRV:6-O-octanoyl-beta-D-fructofuranose'>TRV</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class="sblockDat"><div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]~~</~~div~~><~~/td~~></tr>	+
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PBPX ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])~~</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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [https://pdbe.org/1pyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [https://www.ebi.ac.uk/pdbsum/1pyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyy 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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [https://pdbe.org/1pyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [https://www.ebi.ac.uk/pdbsum/1pyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PBPX_STRR6 PBPX_STRR6]] Penicillin-binding proteins (PBPs) function in the late steps of murein biosynthesis. Beta-lactams inactivate the PBPs by acylating an essential serine residue in the active site of these proteins.	+	[https://www.uniprot.org/uniprot/PBPX_STRR6 PBPX_STRR6] Penicillin-binding proteins (PBPs) function in the late steps of murein biosynthesis. Beta-lactams inactivate the PBPs by acylating an essential serine residue in the active site of these proteins.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Strr6~~]]	+	[[Category: Streptococcus pneumoniae R6]]
-	[[Category: Champelovier, D]]	+	[[Category: Champelovier D]]
-	[[Category: Chesnel, L]]	+	[[Category: Chesnel L]]
-	[[Category: Croize, J]]	+	[[Category: Croize J]]
-	[[Category: Dideberg, O]]	+	[[Category: Dideberg O]]
-	[[Category: Lemaire, D]]	+	[[Category: Lemaire D]]
-	[[Category: Pernot, L]]	+	[[Category: Pernot L]]
-	[[Category: Vernet, T]]	+	[[Category: Vernet T]]
-	[[Category: Zapun, A]]	+	[[Category: Zapun A]]
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Cell wall]]~~	+
-	~~[[Category: Penicillin-binding protein]]~~	+
-	~~[[Category: Peptidoglycan synthesis]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Transpeptidase~~]]	+

OCA at 15:17, 27 October 2021

OCA — Wed, 27 Oct 2021 15:17:54 GMT

OCA at 07:38, 9 December 2020

OCA — Wed, 09 Dec 2020 07:38:59 GMT

←Older revision		Revision as of 07:38, 9 December 2020
Line 1:		Line 1:

	==Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution==		==Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution==
-	<StructureSection load='1pyy' size='340' side='right' caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>	+	<StructureSection load='1pyy' size='340' side='right'caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PYY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=~~OSU~~:~~N-OCTANOYLSUCROSE~~'>~~OSU~~</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRV:'>TRV</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [http://pdbe.org/1pyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [http://www.ebi.ac.uk/pdbsum/1pyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyy ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [http://pdbe.org/1pyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [http://www.ebi.ac.uk/pdbsum/1pyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1pyy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pyy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Strr6]]		[[Category: Strr6]]
	[[Category: Champelovier, D]]		[[Category: Champelovier, D]]

OCA at 08:35, 24 February 2018

OCA — Sat, 24 Feb 2018 08:35:29 GMT

←Older revision		Revision as of 08:35, 24 February 2018
Line 1:		Line 1:
		+
	==Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution==		==Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution==
	<StructureSection load='1pyy' size='340' side='right' caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='1pyy' size='340' side='right' caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [http://pdbe.org/1pyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [http://www.ebi.ac.uk/pdbsum/1pyy 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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [http://pdbe.org/1pyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [http://www.ebi.ac.uk/pdbsum/1pyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/1pyy_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/1pyy_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1pyy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pyy" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Penicillin-binding protein\|Penicillin-binding protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:00, 10 February 2016

OCA — Wed, 10 Feb 2016 04:00:11 GMT

←Older revision		Revision as of 04:00, 10 February 2016
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=1pyy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:10, 11 September 2015

OCA — Fri, 11 Sep 2015 05:10:34 GMT

←Older revision		Revision as of 05:10, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1pyy' size='340' side='right' caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='1pyy' size='340' side='right' caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptococcus_pneumoniae Streptococcus pneumoniae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PYY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OSU:N-OCTANOYLSUCROSE'>OSU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OSU:N-OCTANOYLSUCROSE'>OSU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1313 Streptococcus pneumoniae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [http://www.ebi.ac.uk/pdbsum/1pyy 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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [http://pdbe.org/1pyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [http://www.ebi.ac.uk/pdbsum/1pyy PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1pyy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptococcus pneumoniae~~]]	+	[[Category: Strr6]]
	[[Category: Champelovier, D]]		[[Category: Champelovier, D]]
	[[Category: Chesnel, L]]		[[Category: Chesnel, L]]

OCA at 11:38, 25 December 2014

OCA — Thu, 25 Dec 2014 11:38:55 GMT

←Older revision		Revision as of 11:38, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PYY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PYY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OSU:N-OCTANOYLSUCROSE'>OSU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OSU:N-OCTANOYLSUCROSE'>OSU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 Streptococcus pneumoniae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 Streptococcus pneumoniae])</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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [http://www.ebi.ac.uk/pdbsum/1pyy 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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [http://www.ebi.ac.uk/pdbsum/1pyy PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PBPX_STRR6 PBPX_STRR6]] Penicillin-binding proteins (PBPs) function in the late steps of murein biosynthesis. Beta-lactams inactivate the PBPs by acylating an essential serine residue in the active site of these proteins.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Streptococcus pneumoniae]]		[[Category: Streptococcus pneumoniae]]
-	[[Category: Champelovier, D.]]	+	[[Category: Champelovier, D]]
-	[[Category: Chesnel, L.]]	+	[[Category: Chesnel, L]]
-	[[Category: Croize, J.]]	+	[[Category: Croize, J]]
-	[[Category: Dideberg, O.]]	+	[[Category: Dideberg, O]]
-	[[Category: Lemaire, D.]]	+	[[Category: Lemaire, D]]
-	[[Category: Pernot, L.]]	+	[[Category: Pernot, L]]
-	[[Category: Vernet, T.]]	+	[[Category: Vernet, T]]
-	[[Category: Zapun, A.]]	+	[[Category: Zapun, A]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]
	[[Category: Cell wall]]		[[Category: Cell wall]]

OCA at 20:01, 28 September 2014

OCA — Sun, 28 Sep 2014 20:01:27 GMT

←Older revision		Revision as of 20:01, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1pyy.~~png~~\|~~left~~\|200px]]	+	==Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution==
		+	<StructureSection load='1pyy' size='340' side='right' caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PYY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OSU:N-OCTANOYLSUCROSE'>OSU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 Streptococcus pneumoniae])</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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [http://www.ebi.ac.uk/pdbsum/1pyy 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/py/1pyy_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 ==
		+	PBP2x is a primary determinant of beta-lactams resistance in Streptococcus pneumoniae. Altered PBP2x with multiple mutations have a reduced "affinity" for the antibiotics. An important polymorphism is found in PBP2x sequences from clinical resistant strains. To understand the mechanism of resistance, it is necessary to identify and characterize the relevant substitutions. Many similar PBP2x sequences from resistant isolates have the previously studied T338A mutation, adjacent to the active site Ser337. We report here the structural and functional analysis of the M339F substitution that is found in a subset of these sequences, originating from highly resistant strains. The M339F mutation causes a 4-10-fold reduction of the reaction rate with beta-lactams, depending on the molecular context. In addition, release of the inactivated antibiotic from the active site is up to 3-fold faster as a result from the M339F mutation. These effects measured in vitro are correlated with the level of beta-lactam resistance in vivo conferred by several PBP2x variants. Thus, a single amino acid difference between similar PBP2x from clinical isolates can strongly modulate the degree of beta-lactam resistance. The crystal structure of the double mutant T338A/M339F solved to a resolution of 2.4 A shows a distortion of the active site and a reorientation of the hydroxyl group of the active site Ser337, which can explain the kinetic effects of the mutations.

-	~~{{STRUCTURE_1pyy\| PDB=1pyy \| SCENE= }}~~	+	The structural modifications induced by the M339F substitution in PBP2x from Streptococcus pneumoniae further decreases the susceptibility to beta-lactams of resistant strains.,Chesnel L, Pernot L, Lemaire D, Champelovier D, Croize J, Dideberg O, Vernet T, Zapun A J Biol Chem. 2003 Nov 7;278(45):44448-56. Epub 2003 Aug 15. PMID:12923202<ref>PMID:12923202</ref>

-	~~===Double mutant PBP2x T338A~~/~~M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12923202}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1pyy]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA].~~	+

	==See Also==		==See Also==
	*[[Penicillin-binding protein\|Penicillin-binding protein]]		*[[Penicillin-binding protein\|Penicillin-binding protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012923202<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Streptococcus pneumoniae]]		[[Category: Streptococcus pneumoniae]]
	[[Category: Champelovier, D.]]		[[Category: Champelovier, D.]]

OCA at 16:15, 20 October 2012

OCA — Sat, 20 Oct 2012 16:15:41 GMT

←Older revision		Revision as of 16:15, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1pyy]] is a 1 chain structure ~~of [[Penicillin-binding protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA].	+	[[1pyy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA].

	==See Also==		==See Also==

OCA: Protected "1pyy" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 21:06:31 GMT

Protected "1pyy" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:06, 26 July 2012

←Older revision		Revision as of 15:17, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1pyy' size='340' side='right'caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='1pyy' size='340' side='right'caption='[[1pyy]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1PYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pyy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PYY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRV:'>TRV</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRV:'>TRV</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qme\|1qme]], [[1qmf\|1qmf]], [[1k25\|1k25]], [[1pmd\|1pmd]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBPX ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [~~http~~://pdbe.org/1pyy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pyy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyy 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=1pyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyy OCA], [https://pdbe.org/1pyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pyy RCSB], [https://www.ebi.ac.uk/pdbsum/1pyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PBPX_STRR6 PBPX_STRR6]] Penicillin-binding proteins (PBPs) function in the late steps of murein biosynthesis. Beta-lactams inactivate the PBPs by acylating an essential serine residue in the active site of these proteins.	+	[[https://www.uniprot.org/uniprot/PBPX_STRR6 PBPX_STRR6]] Penicillin-binding proteins (PBPs) function in the late steps of murein biosynthesis. Beta-lactams inactivate the PBPs by acylating an essential serine residue in the active site of these proteins.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]