163l - Revision history

OCA at 06:25, 7 February 2024

2024-02-07T06:25:29Z

←Older revision		Revision as of 06:25, 7 February 2024
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	<StructureSection load='163l' size='340' side='right'caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='163l' size='340' side='right'caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=163L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=163L 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]] 1.8Å</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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [https://pdbe.org/163l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [https://www.ebi.ac.uk/pdbsum/163l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=163l 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [https://pdbe.org/163l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [https://www.ebi.ac.uk/pdbsum/163l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=163l 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=163l 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=163l ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A series of individual alanine mutations has been constructed in the helical region 115 to 123 in phage T4 lysozyme in order to evaluate the contribution to protein stability of the different side-chains within this region. Pairwise alanine mutations and a combination mutant with seven alanine substitutions were constructed to evaluate the additive effects upon structure and stability. Only three residues within this region (Ser117, Leu118 and Leu121) have a substantial influence upon stability (change in free energy of unfolding greater than 1.0 kcal/mol). Replacement of Ser117 with alanine results in an increase in protein stability of 1.27 kcal/mol, apparently due to the release of strain present in the wild-type protein. Replacement of the buried residues Leu118 and Leu121 is destabilizing. Substitution of the remaining six residues with alanine has relatively little effect on stability. This is consistent with prior studies showing that only 20 to 30% of the residues in amphipathic helices in T4 lysozyme are critical for stability. For some of the pairwise alanine mutants the effects on stability are additive. For most of these mutants, however, there is a slight (approximately 0.15 to 0.25 kcal/mol) non-additivity such that the double mutant is more stable than the sum of the constituent single mutants. This effect is consistently observed for residues with positions i, i +4; i.e. adjacent, but in consecutive turns of the helix, suggesting a weak but significant interaction between these amino acid residues. A more pronounced non-additivity (approximately 0.5 kcal/mol) is seen in the seven-alanine combination mutant. This non-additivity is due to a modest "collapse" or "repacking" that occurs for the combination mutants (especially the multiple alanine mutant) but is not possible for the single replacements. The truncation of some side-chains permits an increase in solvent accessibility of main-chain amide and carbonyl groups. This effect is most pronounced for the seven-alanine combination mutant, where two solvent molecules, not present in wild-type, hydrogen bond to main-chain carbonyl groups in the middle region of the helix. It has been suggested that the binding of such water molecules might represent the first step in solvent-mediated unfolding of an alpha-helix. The appearance of ordered solvent, however, appears to have very little effect on stability (approximately less than 0.2 kcal/mol).
-
-	Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme: effects on structure, stability and the binding of solvent.,Blaber M, Baase WA, Gassner N, Matthews BW J Mol Biol. 1995 Feb 17;246(2):317-30. PMID:7869383<ref>PMID:7869383</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 163l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Blaber M]]
-	[[Category: Blaber, M]]	+	[[Category: Matthews BW]]
-	[[Category: Matthews~~, B W~~]]	+

OCA at 10:25, 14 July 2021

2021-07-14T10:25:07Z

←Older revision		Revision as of 10:25, 14 July 2021
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	<StructureSection load='163l' size='340' side='right'caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='163l' size='340' side='right'caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=163L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=163L 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [~~http~~://pdbe.org/163l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/163l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=163l 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [https://pdbe.org/163l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [https://www.ebi.ac.uk/pdbsum/163l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=163l 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 07:19, 10 October 2019

2019-10-10T07:19:23Z

←Older revision		Revision as of 07:19, 10 October 2019
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	==CONTROL OF ENZYME ACTIVITY BY AN ENGINEERED DISULFIDE BOND==		==CONTROL OF ENZYME ACTIVITY BY AN ENGINEERED DISULFIDE BOND==
-	<StructureSection load='163l' size='340' side='right' caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='163l' size='340' side='right'caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L FirstGlance]. <br>		<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L 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/63/163l_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/63/163l_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: Blaber, M]]		[[Category: Blaber, M]]
	[[Category: Matthews, B W]]		[[Category: Matthews, B W]]

OCA at 06:20, 29 November 2017

2017-11-29T06:20:53Z

←Older revision		Revision as of 06:20, 29 November 2017
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	<StructureSection load='163l' size='340' side='right' caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='163l' size='340' side='right' caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[163l]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L 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: Blaber, M]]		[[Category: Blaber, M]]
	[[Category: Matthews, B W]]		[[Category: Matthews, B W]]

OCA at 09:20, 9 August 2017

2017-08-09T09:20:13Z

←Older revision		Revision as of 09:20, 9 August 2017
Line 1:		Line 1:
		+
	==CONTROL OF ENZYME ACTIVITY BY AN ENGINEERED DISULFIDE BOND==		==CONTROL OF ENZYME ACTIVITY BY AN ENGINEERED DISULFIDE BOND==
	<StructureSection load='163l' size='340' side='right' caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='163l' size='340' side='right' caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[163l]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [http://pdbe.org/163l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [http://www.ebi.ac.uk/pdbsum/163l 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [http://pdbe.org/163l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [http://www.ebi.ac.uk/pdbsum/163l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=163l 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=163l 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: Blaber, M]]		[[Category: Blaber, M]]
	[[Category: Matthews, B W]]		[[Category: Matthews, B W]]

OCA at 15:57, 9 September 2015

2015-09-09T15:57:09Z

←Older revision		Revision as of 15:57, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='163l' size='340' side='right' caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='163l' size='340' side='right' caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [http://www.ebi.ac.uk/pdbsum/163l 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [http://pdbe.org/163l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [http://www.ebi.ac.uk/pdbsum/163l 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 163l" 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: Blaber, M]]		[[Category: Blaber, M]]
	[[Category: Matthews, B W]]		[[Category: Matthews, B W]]

OCA at 16:27, 25 December 2014

2014-12-25T16:27:01Z

←Older revision		Revision as of 16:27, 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [http://www.ebi.ac.uk/pdbsum/163l 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [http://www.ebi.ac.uk/pdbsum/163l 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 11:11, 22 December 2014

2014-12-22T11:11:59Z

←Older revision		Revision as of 11:11, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L FirstGlance]. <br>		<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [http://www.ebi.ac.uk/pdbsum/163l 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [http://www.ebi.ac.uk/pdbsum/163l 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: Blaber, M.]]	+	[[Category: Blaber, M]]
-	[[Category: Matthews, B W.]]	+	[[Category: Matthews, B W]]

OCA at 08:33, 23 July 2014

2014-07-23T08:33:41Z

←Older revision		Revision as of 08:33, 23 July 2014
Line 1:		Line 1:
-	[[~~Image~~:163l.~~png\|left~~\|200px]]	+	==CONTROL OF ENZYME ACTIVITY BY AN ENGINEERED DISULFIDE BOND==
		+	<StructureSection load='163l' size='340' side='right' caption='[[163l]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[163l]] 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=163L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=163L 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=163l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=163l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=163l RCSB], [http://www.ebi.ac.uk/pdbsum/163l 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/63/163l_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 ==
		+	A series of individual alanine mutations has been constructed in the helical region 115 to 123 in phage T4 lysozyme in order to evaluate the contribution to protein stability of the different side-chains within this region. Pairwise alanine mutations and a combination mutant with seven alanine substitutions were constructed to evaluate the additive effects upon structure and stability. Only three residues within this region (Ser117, Leu118 and Leu121) have a substantial influence upon stability (change in free energy of unfolding greater than 1.0 kcal/mol). Replacement of Ser117 with alanine results in an increase in protein stability of 1.27 kcal/mol, apparently due to the release of strain present in the wild-type protein. Replacement of the buried residues Leu118 and Leu121 is destabilizing. Substitution of the remaining six residues with alanine has relatively little effect on stability. This is consistent with prior studies showing that only 20 to 30% of the residues in amphipathic helices in T4 lysozyme are critical for stability. For some of the pairwise alanine mutants the effects on stability are additive. For most of these mutants, however, there is a slight (approximately 0.15 to 0.25 kcal/mol) non-additivity such that the double mutant is more stable than the sum of the constituent single mutants. This effect is consistently observed for residues with positions i, i +4; i.e. adjacent, but in consecutive turns of the helix, suggesting a weak but significant interaction between these amino acid residues. A more pronounced non-additivity (approximately 0.5 kcal/mol) is seen in the seven-alanine combination mutant. This non-additivity is due to a modest "collapse" or "repacking" that occurs for the combination mutants (especially the multiple alanine mutant) but is not possible for the single replacements. The truncation of some side-chains permits an increase in solvent accessibility of main-chain amide and carbonyl groups. This effect is most pronounced for the seven-alanine combination mutant, where two solvent molecules, not present in wild-type, hydrogen bond to main-chain carbonyl groups in the middle region of the helix. It has been suggested that the binding of such water molecules might represent the first step in solvent-mediated unfolding of an alpha-helix. The appearance of ordered solvent, however, appears to have very little effect on stability (approximately less than 0.2 kcal/mol).

-	~~{{STRUCTURE_163l\| PDB=163l \| SCENE= }}~~	+	Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme: effects on structure, stability and the binding of solvent.,Blaber M, Baase WA, Gassner N, Matthews BW J Mol Biol. 1995 Feb 17;246(2):317-30. PMID:7869383<ref>PMID:7869383</ref>

-	~~===CONTROL OF ENZYME ACTIVITY BY AN ENGINEERED DISULFIDE BOND===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7869383}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[163l]] 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=163L 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:007869383<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Blaber, M.]]		[[Category: Blaber, M.]]
	[[Category: Matthews, B W.]]		[[Category: Matthews, B W.]]

OCA at 18:53, 20 October 2012

2012-10-20T18:53:34Z

←Older revision		Revision as of 18:53, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[163l]] 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=163L OCA].	+	[[163l]] 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=163L OCA].

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