2ar3 - Revision history

OCA at 09:14, 14 February 2024

2024-02-14T09:14:02Z

←Older revision		Revision as of 09:14, 14 February 2024
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	<StructureSection load='2ar3' size='340' side='right'caption='[[2ar3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2ar3' size='340' side='right'caption='[[2ar3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ar3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var.~~ anthracis~~" (cohn 1872) smith et al. 1946~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ar3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AR3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1yb0\|1yb0]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>sterne ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1392~~ "~~Bacillus cereus var. anthracis~~" ~~(Cohn 1872) Smith et al. 1946])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28]~~ </~~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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [https://pdbe.org/2ar3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [https://www.ebi.ac.uk/pdbsum/2ar3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ar3 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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [https://pdbe.org/2ar3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [https://www.ebi.ac.uk/pdbsum/2ar3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ar3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A6H3AMF3_BACAN A0A6H3AMF3_BACAN]
	== 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=2ar3 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=2ar3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We report a structural and functional analysis of the lambda prophage Ba02 endolysin (PlyL) encoded by the Bacillus anthracis genome. We show that PlyL comprises two autonomously folded domains, an N-terminal catalytic domain and a C-terminal cell wall-binding domain. We determined the crystal structure of the catalytic domain; its three-dimensional fold is related to that of the cell wall amidase, T7 lysozyme, and contains a conserved zinc coordination site and other components of the catalytic machinery. We demonstrate that PlyL is an N-acetylmuramoyl-L-alanine amidase that cleaves the cell wall of several Bacillus species when applied exogenously. We show, unexpectedly, that the catalytic domain of PlyL cleaves more efficiently than the full-length protein, except in the case of Bacillus cereus, and using GFP-tagged cell wall-binding domain, we detected strong binding of the cell wall-binding domain to B. cereus but not to other species tested. We further show that a related endolysin (Ply21) from the B. cereus phage, TP21, shows a similar pattern of behavior. To explain these data, and the species specificity of PlyL, we propose that the C-terminal domain inhibits the activity of the catalytic domain through intramolecular interactions that are relieved upon binding of the C-terminal domain to the cell wall. Furthermore, our data show that (when applied exogenously) targeting of the enzyme to the cell wall is not a prerequisite of its lytic activity, which is inherently high. These results may have broad implications for the design of endolysins as therapeutic agents.
-
-	Structure and lytic activity of a Bacillus anthracis prophage endolysin.,Low LY, Yang C, Perego M, Osterman A, Liddington RC J Biol Chem. 2005 Oct 21;280(42):35433-9. Epub 2005 Aug 15. PMID:16103125<ref>PMID:16103125</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2ar3" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus anthracis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: N-acetylmuramoyl-L-alanine amidase]]~~	+	[[Category: Liddington RC]]
-	[[Category: Liddington~~, R C~~]]	+	[[Category: Low LY]]
-	[[Category: Low~~, L Y~~]]	+	[[Category: Osterman A]]
-	[[Category: Osterman, A]]	+	[[Category: Perego M]]
-	[[Category: Perego, M]]	+	[[Category: Yang C]]
-	[[Category: Yang, C]]	+
-	~~[[Category: Endolysin]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:36, 27 January 2021

2021-01-27T08:36:40Z

←Older revision		Revision as of 08:36, 27 January 2021
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	==E90A mutant structure of PlyL==		==E90A mutant structure of PlyL==
-	<StructureSection load='2ar3' size='340' side='right' caption='[[2ar3]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2ar3' size='340' side='right'caption='[[2ar3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ar3]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2AR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ar3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AR3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yb0\|1yb0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yb0\|1yb0]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sterne ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sterne ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [~~http~~://pdbe.org/2ar3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ar3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ar3 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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [https://pdbe.org/2ar3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [https://www.ebi.ac.uk/pdbsum/2ar3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ar3 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
	[[Category: Liddington, R C]]		[[Category: Liddington, R C]]

OCA at 07:11, 9 May 2018

2018-05-09T07:11:24Z

←Older revision		Revision as of 07:11, 9 May 2018
Line 1:		Line 1:
		+
	==E90A mutant structure of PlyL==		==E90A mutant structure of PlyL==
	<StructureSection load='2ar3' size='340' side='right' caption='[[2ar3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2ar3' size='340' side='right' caption='[[2ar3]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sterne ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sterne ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [http://pdbe.org/2ar3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [http://www.ebi.ac.uk/pdbsum/2ar3 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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [http://pdbe.org/2ar3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [http://www.ebi.ac.uk/pdbsum/2ar3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ar3 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ar/2ar3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ar/2ar3_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 15:24, 9 February 2016

2016-02-09T15:24:09Z

←Older revision		Revision as of 15:24, 9 February 2016
Line 17:		Line 17:
	<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=2ar3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:33, 10 September 2015

2015-09-10T23:33:29Z

←Older revision		Revision as of 23:33, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2ar3' size='340' side='right' caption='[[2ar3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2ar3' size='340' side='right' caption='[[2ar3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ar3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_anthracis Bacillus~~ anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ar3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AR3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yb0\|1yb0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yb0\|1yb0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sterne ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 Bacillus anthracis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sterne ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [http://www.ebi.ac.uk/pdbsum/2ar3 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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [http://pdbe.org/2ar3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [http://www.ebi.ac.uk/pdbsum/2ar3 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 2ar3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus anthracis]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
	[[Category: Liddington, R C]]		[[Category: Liddington, R C]]

OCA at 10:26, 8 January 2015

2015-01-08T10:26:01Z

←Older revision		Revision as of 10:26, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ar3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AR3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ar3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AR3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yb0\|1yb0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yb0\|1yb0]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sterne ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 Bacillus anthracis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sterne ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 Bacillus anthracis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [http://www.ebi.ac.uk/pdbsum/2ar3 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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [http://www.ebi.ac.uk/pdbsum/2ar3 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 33:		Line 33:
	[[Category: Bacillus anthracis]]		[[Category: Bacillus anthracis]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
-	[[Category: Liddington, R C.]]	+	[[Category: Liddington, R C]]
-	[[Category: Low, L Y.]]	+	[[Category: Low, L Y]]
-	[[Category: Osterman, A.]]	+	[[Category: Osterman, A]]
-	[[Category: Perego, M.]]	+	[[Category: Perego, M]]
-	[[Category: Yang, C.]]	+	[[Category: Yang, C]]
	[[Category: Endolysin]]		[[Category: Endolysin]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 01:11, 30 September 2014

2014-09-30T01:11:21Z

←Older revision		Revision as of 01:11, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2ar3.~~png~~\|~~left~~\|200px]]	+	==E90A mutant structure of PlyL==
		+	<StructureSection load='2ar3' size='340' side='right' caption='[[2ar3]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ar3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AR3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yb0\|1yb0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sterne ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 Bacillus anthracis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </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=2ar3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ar3 RCSB], [http://www.ebi.ac.uk/pdbsum/2ar3 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/ar/2ar3_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 ==
		+	We report a structural and functional analysis of the lambda prophage Ba02 endolysin (PlyL) encoded by the Bacillus anthracis genome. We show that PlyL comprises two autonomously folded domains, an N-terminal catalytic domain and a C-terminal cell wall-binding domain. We determined the crystal structure of the catalytic domain; its three-dimensional fold is related to that of the cell wall amidase, T7 lysozyme, and contains a conserved zinc coordination site and other components of the catalytic machinery. We demonstrate that PlyL is an N-acetylmuramoyl-L-alanine amidase that cleaves the cell wall of several Bacillus species when applied exogenously. We show, unexpectedly, that the catalytic domain of PlyL cleaves more efficiently than the full-length protein, except in the case of Bacillus cereus, and using GFP-tagged cell wall-binding domain, we detected strong binding of the cell wall-binding domain to B. cereus but not to other species tested. We further show that a related endolysin (Ply21) from the B. cereus phage, TP21, shows a similar pattern of behavior. To explain these data, and the species specificity of PlyL, we propose that the C-terminal domain inhibits the activity of the catalytic domain through intramolecular interactions that are relieved upon binding of the C-terminal domain to the cell wall. Furthermore, our data show that (when applied exogenously) targeting of the enzyme to the cell wall is not a prerequisite of its lytic activity, which is inherently high. These results may have broad implications for the design of endolysins as therapeutic agents.

-	~~{{STRUCTURE_2ar3\| PDB=2ar3 \| SCENE= }}~~	+	Structure and lytic activity of a Bacillus anthracis prophage endolysin.,Low LY, Yang C, Perego M, Osterman A, Liddington RC J Biol Chem. 2005 Oct 21;280(42):35433-9. Epub 2005 Aug 15. PMID:16103125<ref>PMID:16103125</ref>

-	~~===E90A mutant structure~~ of ~~PlyL===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16103125}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2ar3]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_anthracis Bacillus anthracis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016103125<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus anthracis]]		[[Category: Bacillus anthracis]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]

OCA: Protected "2ar3" [edit=sysop:move=sysop]

2013-01-06T10:27:02Z

Protected "2ar3" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:27, 6 January 2013

OCA at 10:26, 6 January 2013

2013-01-06T10:26:57Z

←Older revision		Revision as of 10:26, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2ar3.png\|left\|200px]]		[[Image:2ar3.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2ar3", 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_2ar3\| PDB=2ar3 \| SCENE= }}		{{STRUCTURE_2ar3\| PDB=2ar3 \| SCENE= }}

	===E90A mutant structure of PlyL===		===E90A mutant structure of PlyL===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16103125}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16103125 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16103125}}		{{ABSTRACT_PUBMED_16103125}}

	==About this Structure==		==About this Structure==
-	~~2AR3~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA].	+	[[2ar3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16103125~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016103125</ref><references group="xtra"/>
	[[Category: Bacillus anthracis]]		[[Category: Bacillus anthracis]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
Line 32:		Line 20:
	[[Category: Yang, C.]]		[[Category: Yang, C.]]
	[[Category: Endolysin]]		[[Category: Endolysin]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 10:48:17 2009''~~	+

OCA at 08:48, 17 February 2009

2009-02-17T08:48:18Z

←Older revision		Revision as of 08:48, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2AR3 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA].	+	2AR3 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AR3 OCA].

	==Reference==		==Reference==
-	~~Structure and lytic activity of a Bacillus anthracis prophage endolysin., Low LY, Yang C, Perego M, Osterman A, Liddington RC, J Biol Chem. 2005 Oct 21;280(42):35433-9. Epub 2005 Aug 15.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16103125 16103125]~~	+	<ref group="xtra">PMID:16103125</ref><references group="xtra"/>
	[[Category: Bacillus anthracis]]		[[Category: Bacillus anthracis]]
	[[Category: N-acetylmuramoyl-L-alanine amidase]]		[[Category: N-acetylmuramoyl-L-alanine amidase]]
-	[[Category: Single protein]]
	[[Category: Liddington, R C.]]		[[Category: Liddington, R C.]]
	[[Category: Low, L Y.]]		[[Category: Low, L Y.]]
Line 34:		Line 33:
	[[Category: Endolysin]]		[[Category: Endolysin]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 14~~:46:~~10 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:48:17 2009''