195l - Revision history

OCA at 06:26, 7 February 2024

2024-02-07T06:26:21Z

←Older revision		Revision as of 06:26, 7 February 2024
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	<StructureSection load='195l' size='340' side='right'caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='195l' size='340' side='right'caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpt4 Bpt4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=195L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=195L FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BME:BETA~~-~~MERCAPTOETHANOL'>BME</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.9Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Lysozyme Lysozyme]~~, ~~with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [https://pdbe.org/195l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [https://www.ebi.ac.uk/pdbsum/195l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=195l 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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [https://pdbe.org/195l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [https://www.ebi.ac.uk/pdbsum/195l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=195l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~LYS_BPT4 LYS_BPT4~~]~~] Helps~~ to ~~release~~ the mature ~~phage~~ particles ~~from~~ the cell ~~wall by breaking~~ down the peptidoglycan.	+	[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		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=195l 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=195l ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Previous analysis of randomly generated multiple mutations within the core of bacteriophage T4 lysozyme suggested that the "large-to-small" substitution Leu121 to Ala (L121A) and the spatially adjacent "small-to-large" substitution Ala129 to Met (A129M) might be mutually compensating. To test this hypothesis, the individual variants L121A and A129M were generated, as well as the double "size-switch" mutant L121A/A129M. To make the interchange symmetrical, the combination of L121A with A129L to give L121A/A129L was also constructed. The single mutations were all destabilizing. Somewhat surprisingly, the small-to-large substitutions, which increase hydrophobic stabilization but can also introduce strain, were less deleterious than the large-to-small replacements. Both Ala129 --> Leu and Ala129 --> Met offset the destabilization of L121A by about 50%. Also, in contrast to typical Leu --> Ala core substitutions, which destabilize by 2 to 5 kcal/mol, Leu121 --> Ala slightly stabilized A129L and A129M. Crystal structure analysis showed that a combination of side-chain and backbone adjustments partially accommodated changes in side-chain volume, but only to a limited degree. For example, the cavity that was created by the Leu121 to Ala replacement actually became larger in L121A/A129L. The results demonstrate that the destabilization associated with a change in volume of one core residue can be specifically compensated by an offsetting volume change in an adjacent residue. It appears, however, that complete compensation is unlikely because it is difficult to reconstitute an equivalent set of interactions. The relatively slow evolution of core relative to surface residues appears, therefore, to be due to two factors. First, a mutation in a single core residue that results in a substantial change in size will normally lead to a significant loss in stability. Such mutations will presumably be selected against. Second, if a change in bulk does occur in a buried residue, it cannot normally be fully compensated by a mutation of an adjacent residue. Thus, the most probable response will tend to be reversion to the parent protein.
-
-	Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme.,Baldwin E, Xu J, Hajiseyedjavadi O, Baase WA, Matthews BW J Mol Biol. 1996 Jun 14;259(3):542-59. PMID:8676387<ref>PMID:8676387</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 195l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Baldwin E]]
-	[[Category: Baldwin, E]]	+	[[Category: Hajiseyedjavadi O]]
-	[[Category: Hajiseyedjavadi, O]]	+	[[Category: Matthews BW]]
-	[[Category: Matthews~~, B W~~]]	+	[[Category: Xu J]]
-	[[Category: Xu, J]]	+
-	~~[[Category: Cavity]]~~	+
-	~~[[Category: Core-packing]]~~	+
-	~~[[Category: Protein stability~~]]	+

OCA at 10:25, 14 July 2021

2021-07-14T10:25:31Z

←Older revision		Revision as of 10:25, 14 July 2021
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	<StructureSection load='195l' size='340' side='right'caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='195l' size='340' side='right'caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=195L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=195L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [~~http~~://pdbe.org/195l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/195l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=195l 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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [https://pdbe.org/195l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [https://www.ebi.ac.uk/pdbsum/195l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=195l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.	+	[[https://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:00, 10 October 2019

2019-10-10T07:00:34Z

←Older revision		Revision as of 07:00, 10 October 2019
Line 1:		Line 1:

	==THERMODYNAMIC AND STRUCTURAL COMPENSATION IN "SIZE-SWITCH" CORE-REPACKING VARIANTS OF T4 LYSOZYME==		==THERMODYNAMIC AND STRUCTURAL COMPENSATION IN "SIZE-SWITCH" CORE-REPACKING VARIANTS OF T4 LYSOZYME==
-	<StructureSection load='195l' size='340' side='right' caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='195l' size='340' side='right'caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>		<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/95/195l_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/95/195l_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 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baldwin, E]]		[[Category: Baldwin, E]]

OCA at 06:21, 29 November 2017

2017-11-29T06:21:39Z

←Older revision		Revision as of 06:21, 29 November 2017
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	<StructureSection load='195l' size='340' side='right' caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='195l' size='340' side='right' caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baldwin, E]]		[[Category: Baldwin, E]]

OCA at 09:25, 9 August 2017

2017-08-09T09:25:43Z

←Older revision		Revision as of 09:25, 9 August 2017
Line 1:		Line 1:
		+
	==THERMODYNAMIC AND STRUCTURAL COMPENSATION IN "SIZE-SWITCH" CORE-REPACKING VARIANTS OF T4 LYSOZYME==		==THERMODYNAMIC AND STRUCTURAL COMPENSATION IN "SIZE-SWITCH" CORE-REPACKING VARIANTS OF T4 LYSOZYME==
	<StructureSection load='195l' size='340' side='right' caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='195l' size='340' side='right' caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [http://pdbe.org/195l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [http://www.ebi.ac.uk/pdbsum/195l 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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [http://pdbe.org/195l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [http://www.ebi.ac.uk/pdbsum/195l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=195l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		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=195l ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baldwin, E]]		[[Category: Baldwin, E]]

OCA at 16:06, 9 September 2015

2015-09-09T16:06:20Z

←Older revision		Revision as of 16:06, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='195l' size='340' side='right' caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='195l' size='340' side='right' caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t4 Enterobacteria phage t4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [http://www.ebi.ac.uk/pdbsum/195l 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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [http://pdbe.org/195l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [http://www.ebi.ac.uk/pdbsum/195l PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 195l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Baldwin, E]]		[[Category: Baldwin, E]]

OCA at 13:54, 25 December 2014

2014-12-25T13:54:13Z

←Older revision		Revision as of 13:54, 25 December 2014
Line 7:		Line 7:
	<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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [http://www.ebi.ac.uk/pdbsum/195l 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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [http://www.ebi.ac.uk/pdbsum/195l PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:55, 22 December 2014

2014-12-22T09:55:25Z

←Older revision		Revision as of 09:55, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>		<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [http://www.ebi.ac.uk/pdbsum/195l 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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [http://www.ebi.ac.uk/pdbsum/195l 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 34:		Line 34:
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Baldwin, E.]]	+	[[Category: Baldwin, E]]
-	[[Category: Hajiseyedjavadi, O.]]	+	[[Category: Hajiseyedjavadi, O]]
-	[[Category: Matthews, B W.]]	+	[[Category: Matthews, B W]]
-	[[Category: Xu, J.]]	+	[[Category: Xu, J]]
	[[Category: Cavity]]		[[Category: Cavity]]
	[[Category: Core-packing]]		[[Category: Core-packing]]
	[[Category: Protein stability]]		[[Category: Protein stability]]

OCA at 08:37, 23 July 2014

2014-07-23T08:37:45Z

←Older revision		Revision as of 08:37, 23 July 2014
Line 1:		Line 1:
-	[[~~Image~~:195l.~~png\|left~~\|200px]]	+	==THERMODYNAMIC AND STRUCTURAL COMPENSATION IN "SIZE-SWITCH" CORE-REPACKING VARIANTS OF T4 LYSOZYME==
		+	<StructureSection load='195l' size='340' side='right' caption='[[195l]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[195l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=195L FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=195l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=195l RCSB], [http://www.ebi.ac.uk/pdbsum/195l 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/95/195l_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 ==
		+	Previous analysis of randomly generated multiple mutations within the core of bacteriophage T4 lysozyme suggested that the "large-to-small" substitution Leu121 to Ala (L121A) and the spatially adjacent "small-to-large" substitution Ala129 to Met (A129M) might be mutually compensating. To test this hypothesis, the individual variants L121A and A129M were generated, as well as the double "size-switch" mutant L121A/A129M. To make the interchange symmetrical, the combination of L121A with A129L to give L121A/A129L was also constructed. The single mutations were all destabilizing. Somewhat surprisingly, the small-to-large substitutions, which increase hydrophobic stabilization but can also introduce strain, were less deleterious than the large-to-small replacements. Both Ala129 --> Leu and Ala129 --> Met offset the destabilization of L121A by about 50%. Also, in contrast to typical Leu --> Ala core substitutions, which destabilize by 2 to 5 kcal/mol, Leu121 --> Ala slightly stabilized A129L and A129M. Crystal structure analysis showed that a combination of side-chain and backbone adjustments partially accommodated changes in side-chain volume, but only to a limited degree. For example, the cavity that was created by the Leu121 to Ala replacement actually became larger in L121A/A129L. The results demonstrate that the destabilization associated with a change in volume of one core residue can be specifically compensated by an offsetting volume change in an adjacent residue. It appears, however, that complete compensation is unlikely because it is difficult to reconstitute an equivalent set of interactions. The relatively slow evolution of core relative to surface residues appears, therefore, to be due to two factors. First, a mutation in a single core residue that results in a substantial change in size will normally lead to a significant loss in stability. Such mutations will presumably be selected against. Second, if a change in bulk does occur in a buried residue, it cannot normally be fully compensated by a mutation of an adjacent residue. Thus, the most probable response will tend to be reversion to the parent protein.

-	~~{{STRUCTURE_195l\| PDB=195l \| SCENE= }}~~	+	Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme.,Baldwin E, Xu J, Hajiseyedjavadi O, Baase WA, Matthews BW J Mol Biol. 1996 Jun 14;259(3):542-59. PMID:8676387<ref>PMID:8676387</ref>

-	~~===THERMODYNAMIC AND STRUCTURAL COMPENSATION IN "SIZE-SWITCH" CORE-REPACKING VARIANTS OF T4 LYSOZYME===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8676387}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[195l]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Hen Egg-White (HEW)~~ Lysozyme\|~~Hen Egg-White (HEW)~~ Lysozyme]]	+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008676387<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 17:29, 20 October 2012

2012-10-20T17:29:18Z

←Older revision		Revision as of 17:29, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[195l]] is a 1 chain structure ~~of [[Hen Egg-White (HEW) Lysozyme]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA].	+	[[195l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195L OCA].

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