1kni - Revision history

OCA at 06:05, 3 April 2024

OCA — Wed, 03 Apr 2024 06:05:45 GMT

←Older revision		Revision as of 06:05, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='1kni' size='340' side='right'caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1kni' size='340' side='right'caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KNI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KNI 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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [https://pdbe.org/1kni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [https://www.ebi.ac.uk/pdbsum/1kni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kni 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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [https://pdbe.org/1kni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [https://www.ebi.ac.uk/pdbsum/1kni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kni 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=1kni 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=1kni ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The engineered disulfide bridge between residues 21 and 142 of phage T4 lysozyme spans the active-site cleft and can be used as a switch to control the activity of the enzyme (Matsumura, M. & Matthews, B.W., 1989, Science 243, 792-794). In the oxidized form the disulfide increases the melting temperature of the protein by 11 degrees C at pH 2. The crystal structure of this mutant lysozyme has been determined in both the reduced and oxidized forms. In the reduced form, the crystal structure of the mutant is shown to be extremely similar to that of wild type. In the oxidized form, however, the formation of the disulfide bridge causes the alpha-carbons of Cys 21 and Cys 142, on opposite sides of the active-site cleft, to move toward each other by 2.5 A. In association with this movement, the amino-terminal domain of the protein undergoes a rigid-body rotation of 5.1 degrees relative to the carboxy-terminal domain. This rotation occurs about an axis passing through the junction of the amino-terminal and carboxy-terminal domains and is also close to the axis that best fits the apparent thermal motion of the amino-terminal domain seen previously in crystals of wild-type lysozyme. Even though the engineered Cys 21-Cys 142 disulfide links together the amino-terminal and carboxy-terminal domains of T4 lysozyme, it does not reduce the apparent mobility of the one domain relative to the other. The pronounced "hinge-bending" mobility of the amino-terminal domain that is suggested by the crystallographic thermal parameters of wild-type lysozyme persists in the oxidized (and reduced) mutant structures. In the immediate vicinity of the introduced disulfide bridge the mutant structure is more mobile (or disordered) than wild type, so much so that the exact conformation of Cys 21 remains obscure. As with the previously described disulfide bridge between residues 9 and 164 of T4 lysozyme (Pjura, P.E., Matsumura, M., Wozniak, J.A., & Matthews, B.W., 1990, Biochemistry 29, 2592-2598), the engineered cross-link substantially enhances the stability of the protein without making the folded structure more rigid.
-
-	Structure of a stabilizing disulfide bridge mutant that closes the active-site cleft of T4 lysozyme.,Jacobson RH, Matsumura M, Faber HR, Matthews BW Protein Sci. 1992 Jan;1(1):46-57. PMID:1304882<ref>PMID:1304882</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kni" 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: Faber HR]]
-	[[Category: Faber~~, H R~~]]	+	[[Category: Jacobson RH]]
-	[[Category: Jacobson~~, R H~~]]	+	[[Category: Matsumura M]]
-	[[Category: Matsumura, M]]	+	[[Category: Matthews BW]]
-	[[Category: Matthews~~, B W]]~~	+
-	~~[[Category: Bacteriolytic enzyme]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 14:43, 27 October 2021

OCA — Wed, 27 Oct 2021 14:43:11 GMT

←Older revision		Revision as of 14:43, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1kni' size='340' side='right'caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1kni' size='340' side='right'caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1KNI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KNI 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='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~~://proteopedia.org/fgij/fg.htm?mol=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [~~http~~://pdbe.org/1kni PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kni PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kni 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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [https://pdbe.org/1kni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [https://www.ebi.ac.uk/pdbsum/1kni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kni 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 11:00, 22 July 2020

OCA — Wed, 22 Jul 2020 11:00:29 GMT

←Older revision		Revision as of 11:00, 22 July 2020
Line 3:		Line 3:
	<StructureSection load='1kni' size='340' side='right'caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1kni' size='340' side='right'caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KNI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1KNI 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'>[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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [http://pdbe.org/1kni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [http://www.ebi.ac.uk/pdbsum/1kni PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kni ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [http://pdbe.org/1kni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [http://www.ebi.ac.uk/pdbsum/1kni PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kni ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 13:05, 17 July 2019

OCA — Wed, 17 Jul 2019 13:05:43 GMT

←Older revision		Revision as of 13:05, 17 July 2019
Line 1:		Line 1:

	==Stabilizing Disulfide Bridge Mutant of T4 Lysozyme==		==Stabilizing Disulfide Bridge Mutant of T4 Lysozyme==
-	<StructureSection load='1kni' size='340' side='right' caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1kni' size='340' side='right'caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KNI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KNI 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/kn/1kni_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kn/1kni_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: Faber, H R]]		[[Category: Faber, H R]]

OCA at 07:20, 11 October 2017

OCA — Wed, 11 Oct 2017 07:20:59 GMT

←Older revision		Revision as of 07:20, 11 October 2017
Line 1:		Line 1:
		+
	==Stabilizing Disulfide Bridge Mutant of T4 Lysozyme==		==Stabilizing Disulfide Bridge Mutant of T4 Lysozyme==
	<StructureSection load='1kni' size='340' side='right' caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1kni' size='340' side='right' caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 5:		Line 6:
	</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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [http://pdbe.org/1kni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [http://www.ebi.ac.uk/pdbsum/1kni 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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [http://pdbe.org/1kni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [http://www.ebi.ac.uk/pdbsum/1kni PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kni 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=1kni ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:47, 11 September 2015

OCA — Fri, 11 Sep 2015 12:47:52 GMT

←Older revision		Revision as of 12:47, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1kni' size='340' side='right' caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1kni' size='340' side='right' caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KNI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KNI 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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [http://www.ebi.ac.uk/pdbsum/1kni 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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [http://pdbe.org/1kni PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [http://www.ebi.ac.uk/pdbsum/1kni 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 1kni" 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: Faber, H R]]		[[Category: Faber, H R]]

OCA at 16:39, 25 December 2014

OCA — Thu, 25 Dec 2014 16:39:44 GMT

←Older revision		Revision as of 16:39, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KNI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KNI 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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [http://www.ebi.ac.uk/pdbsum/1kni 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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [http://www.ebi.ac.uk/pdbsum/1kni 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: Faber, H R.]]	+	[[Category: Faber, H R]]
-	[[Category: Jacobson, R H.]]	+	[[Category: Jacobson, R H]]
-	[[Category: Matsumura, M.]]	+	[[Category: Matsumura, M]]
-	[[Category: Matthews, B W.]]	+	[[Category: Matthews, B W]]
	[[Category: Bacteriolytic enzyme]]		[[Category: Bacteriolytic enzyme]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 14:55, 28 September 2014

OCA — Sun, 28 Sep 2014 14:55:07 GMT

←Older revision		Revision as of 14:55, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1kni.~~png\|left~~\|200px]]	+	==Stabilizing Disulfide Bridge Mutant of T4 Lysozyme==
		+	<StructureSection load='1kni' size='340' side='right' caption='[[1kni]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kni]] 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=1KNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KNI 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=1kni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kni OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kni RCSB], [http://www.ebi.ac.uk/pdbsum/1kni 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/kn/1kni_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 ==
		+	The engineered disulfide bridge between residues 21 and 142 of phage T4 lysozyme spans the active-site cleft and can be used as a switch to control the activity of the enzyme (Matsumura, M. & Matthews, B.W., 1989, Science 243, 792-794). In the oxidized form the disulfide increases the melting temperature of the protein by 11 degrees C at pH 2. The crystal structure of this mutant lysozyme has been determined in both the reduced and oxidized forms. In the reduced form, the crystal structure of the mutant is shown to be extremely similar to that of wild type. In the oxidized form, however, the formation of the disulfide bridge causes the alpha-carbons of Cys 21 and Cys 142, on opposite sides of the active-site cleft, to move toward each other by 2.5 A. In association with this movement, the amino-terminal domain of the protein undergoes a rigid-body rotation of 5.1 degrees relative to the carboxy-terminal domain. This rotation occurs about an axis passing through the junction of the amino-terminal and carboxy-terminal domains and is also close to the axis that best fits the apparent thermal motion of the amino-terminal domain seen previously in crystals of wild-type lysozyme. Even though the engineered Cys 21-Cys 142 disulfide links together the amino-terminal and carboxy-terminal domains of T4 lysozyme, it does not reduce the apparent mobility of the one domain relative to the other. The pronounced "hinge-bending" mobility of the amino-terminal domain that is suggested by the crystallographic thermal parameters of wild-type lysozyme persists in the oxidized (and reduced) mutant structures. In the immediate vicinity of the introduced disulfide bridge the mutant structure is more mobile (or disordered) than wild type, so much so that the exact conformation of Cys 21 remains obscure. As with the previously described disulfide bridge between residues 9 and 164 of T4 lysozyme (Pjura, P.E., Matsumura, M., Wozniak, J.A., & Matthews, B.W., 1990, Biochemistry 29, 2592-2598), the engineered cross-link substantially enhances the stability of the protein without making the folded structure more rigid.

-	~~{{STRUCTURE_1kni\| PDB=1kni \| SCENE= }}~~	+	Structure of a stabilizing disulfide bridge mutant that closes the active-site cleft of T4 lysozyme.,Jacobson RH, Matsumura M, Faber HR, Matthews BW Protein Sci. 1992 Jan;1(1):46-57. PMID:1304882<ref>PMID:1304882</ref>

-	~~===Stabilizing Disulfide Bridge Mutant~~ of ~~T4 Lysozyme===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_1304882}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1kni]] 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=1KNI 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:001304882<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]

OCA at 19:00, 20 October 2012

OCA — Sat, 20 Oct 2012 19:00:27 GMT

←Older revision		Revision as of 19:00, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1kni]] 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=1KNI OCA].	+	[[1kni]] 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=1KNI OCA].

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

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

OCA — Fri, 27 Jul 2012 05:59:08 GMT

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

←Older revision

Revision as of 05:59, 27 July 2012