1l92 - Revision history

OCA at 07:30, 14 February 2024

OCA — Wed, 14 Feb 2024 07:30:53 GMT

←Older revision		Revision as of 07:30, 14 February 2024
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	<StructureSection load='1l92' size='340' side='right'caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1l92' size='340' side='right'caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L92 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]] 1.7Å</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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [https://pdbe.org/1l92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [https://www.ebi.ac.uk/pdbsum/1l92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l92 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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [https://pdbe.org/1l92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [https://www.ebi.ac.uk/pdbsum/1l92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l92 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]]
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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=1l92 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=1l92 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Two bulky amino acids within the core of phage T4 lysozyme have each been replaced in turn with a series of hydrophobic amino acids. In one set of experiments, Leu99 was replaced with Phe, Met, Ile, Val and Ala. In the second series, Phe153 was replaced with Leu, Met, Ile, Val and Ala. The double mutant in which both Leu99 and Phe153 were replaced with alanine was also constructed. The change in stability of the protein associated with each substitution and the crystal structure of each variant have been determined. In the case of replacements at position 99 the protein behaves in a relatively rigid manner, and changes very little in response to substitutions. In contrast, the protein is more flexible and adjusts much more in response to substitutions of Phe153. In both cases there is a roughly linear dependence between the stability of the mutant protein relative to wild-type (delta delta G) and the difference in the hydrophobic strength of the amino acids involved in the substitution based on solvent transfer measurements (delta delta Gtr). The change in delta delta G is, however, much greater than delta delta Gtr. For the Phe153 replacements the discrepancy is about 1.9-fold, while for the Leu99 series it is about 2.6-fold. Mutants such as Leu99-->Ala, for which the protein remains essentially rigid, tend to create larger cavities and so incur a larger energy of destabilization. Mutants such as Phe153-->Ala, for which the protein structure tends to relax, result in smaller cavities and so are less destabilized. Mutants L99I and L99V are less stable than expected from considerations of transfer free energy and cavity formation due to introduced strain caused by the replacement of Leu99 with a residue of different shape. Mutant F153L is more stable than the reference wild-type, even though the transfer free energy of Leu is less than that of Phe. The increase in stability is apparently due to torsional strain in the side-chain of Phe153 that is present in wild-type lysozyme, but is relieved in the mutant structure.
-
-	Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences.,Eriksson AE, Baase WA, Matthews BW J Mol Biol. 1993 Feb 5;229(3):747-69. PMID:8433369<ref>PMID:8433369</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1l92" 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: Eriksson AE]]
-	[[Category: Eriksson~~, A E~~]]	+	[[Category: Matthews BW]]
-	[[Category: Matthews~~, B W~~]]	+

OCA at 06:41, 18 August 2021

OCA — Wed, 18 Aug 2021 06:41:36 GMT

←Older revision		Revision as of 06:41, 18 August 2021
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	<StructureSection load='1l92' size='340' side='right'caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1l92' size='340' side='right'caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1L92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L92 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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [~~http~~://pdbe.org/1l92 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1l92 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1l92 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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [https://pdbe.org/1l92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [https://www.ebi.ac.uk/pdbsum/1l92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l92 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 12:41, 13 November 2019

OCA — Wed, 13 Nov 2019 12:41:57 GMT

←Older revision		Revision as of 12:41, 13 November 2019
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	==SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES==		==SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES==
-	<StructureSection load='1l92' size='340' side='right' caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1l92' size='340' side='right'caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L92 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L92 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/l9/1l92_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l9/1l92_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>
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	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Eriksson, A E]]		[[Category: Eriksson, A E]]
	[[Category: Matthews, B W]]		[[Category: Matthews, B W]]

OCA at 10:57, 18 October 2017

OCA — Wed, 18 Oct 2017 10:57:50 GMT

←Older revision		Revision as of 10:57, 18 October 2017
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		+
	==SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES==		==SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES==
	<StructureSection load='1l92' size='340' side='right' caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1l92' size='340' side='right' caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>
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	</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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [http://pdbe.org/1l92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [http://www.ebi.ac.uk/pdbsum/1l92 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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [http://pdbe.org/1l92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [http://www.ebi.ac.uk/pdbsum/1l92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l92 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=1l92 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:28, 11 September 2015

OCA — Fri, 11 Sep 2015 16:28:46 GMT

←Older revision		Revision as of 16:28, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1l92' size='340' side='right' caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1l92' size='340' side='right' caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L92 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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [http://www.ebi.ac.uk/pdbsum/1l92 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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [http://pdbe.org/1l92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [http://www.ebi.ac.uk/pdbsum/1l92 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1l92" 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: Eriksson, A E]]		[[Category: Eriksson, A E]]
	[[Category: Matthews, B W]]		[[Category: Matthews, B W]]

OCA at 19:00, 25 December 2014

OCA — Thu, 25 Dec 2014 19:00:48 GMT

←Older revision		Revision as of 19:00, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L92 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L92 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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [http://www.ebi.ac.uk/pdbsum/1l92 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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [http://www.ebi.ac.uk/pdbsum/1l92 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]]
Line 34:		Line 36:
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Eriksson, A E.]]	+	[[Category: Eriksson, A E]]
-	[[Category: Matthews, B W.]]	+	[[Category: Matthews, B W]]

OCA at 18:47, 28 September 2014

OCA — Sun, 28 Sep 2014 18:47:15 GMT

←Older revision		Revision as of 18:47, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1l92.~~png\|left~~\|200px]]	+	==SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES==
		+	<StructureSection load='1l92' size='340' side='right' caption='[[1l92]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1l92]] 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=1L92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L92 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=1l92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l92 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l92 RCSB], [http://www.ebi.ac.uk/pdbsum/1l92 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/l9/1l92_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 ==
		+	Two bulky amino acids within the core of phage T4 lysozyme have each been replaced in turn with a series of hydrophobic amino acids. In one set of experiments, Leu99 was replaced with Phe, Met, Ile, Val and Ala. In the second series, Phe153 was replaced with Leu, Met, Ile, Val and Ala. The double mutant in which both Leu99 and Phe153 were replaced with alanine was also constructed. The change in stability of the protein associated with each substitution and the crystal structure of each variant have been determined. In the case of replacements at position 99 the protein behaves in a relatively rigid manner, and changes very little in response to substitutions. In contrast, the protein is more flexible and adjusts much more in response to substitutions of Phe153. In both cases there is a roughly linear dependence between the stability of the mutant protein relative to wild-type (delta delta G) and the difference in the hydrophobic strength of the amino acids involved in the substitution based on solvent transfer measurements (delta delta Gtr). The change in delta delta G is, however, much greater than delta delta Gtr. For the Phe153 replacements the discrepancy is about 1.9-fold, while for the Leu99 series it is about 2.6-fold. Mutants such as Leu99-->Ala, for which the protein remains essentially rigid, tend to create larger cavities and so incur a larger energy of destabilization. Mutants such as Phe153-->Ala, for which the protein structure tends to relax, result in smaller cavities and so are less destabilized. Mutants L99I and L99V are less stable than expected from considerations of transfer free energy and cavity formation due to introduced strain caused by the replacement of Leu99 with a residue of different shape. Mutant F153L is more stable than the reference wild-type, even though the transfer free energy of Leu is less than that of Phe. The increase in stability is apparently due to torsional strain in the side-chain of Phe153 that is present in wild-type lysozyme, but is relieved in the mutant structure.

-	~~{{STRUCTURE_1l92\| PDB=1l92 \| SCENE= }}~~	+	Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences.,Eriksson AE, Baase WA, Matthews BW J Mol Biol. 1993 Feb 5;229(3):747-69. PMID:8433369<ref>PMID:8433369</ref>

-	~~===SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8433369}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1l92]] 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=1L92 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:008433369<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Eriksson, A E.]]		[[Category: Eriksson, A E.]]
	[[Category: Matthews, B W.]]		[[Category: Matthews, B W.]]

OCA at 20:17, 20 October 2012

OCA — Sat, 20 Oct 2012 20:17:54 GMT

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

	==About this Structure==		==About this Structure==
-	[[1l92]] 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=1L92 OCA].	+	[[1l92]] 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=1L92 OCA].

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

OCA: Protected "1l92" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 10:01:46 GMT

Protected "1l92" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:01, 27 July 2012

OCA at 10:01, 27 July 2012

OCA — Fri, 27 Jul 2012 10:01:45 GMT

←Older revision		Revision as of 10:01, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1l92.png\|left\|200px]]		[[Image:1l92.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1l92\| PDB=1l92 \| SCENE= }}		{{STRUCTURE_1l92\| PDB=1l92 \| SCENE= }}

	===SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES===		===SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8433369}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8433369 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8433369}}		{{ABSTRACT_PUBMED_8433369}}

	==About this Structure==		==About this Structure==
-	~~1L92~~ is a 1 chain structure of 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=1L92 OCA].	+	[[1l92]] 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=1L92 OCA].
		+
		+	==See Also==
		+	*[[Hen Egg-White (HEW) Lysozyme\|Hen Egg-White (HEW) Lysozyme]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8433369~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008433369</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Eriksson, A E.]]		[[Category: Eriksson, A E.]]
	[[Category: Matthews, B W.]]		[[Category: Matthews, B W.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:47:57 2009''