5v7e - Revision history

OCA at 13:43, 4 October 2023

2023-10-04T13:43:14Z

←Older revision		Revision as of 13:43, 4 October 2023
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	<StructureSection load='5v7e' size='340' side='right'caption='[[5v7e]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='5v7e' size='340' side='right'caption='[[5v7e]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7e]] 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=5V7E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V7E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7e]] 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=5V7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V7E FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=HED:2~~-~~HYDROXYETHYL+DISULFIDE'>HED</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.36Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=3CT:3-CHLORO-L-TYROSINE'>3CT</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3CT:3-CHLORO-L-TYROSINE'>3CT</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[5v7d\|5v7d]], [[5v7f\|5v7f]]</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=5v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7e OCA], [https://pdbe.org/5v7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v7e RCSB], [https://www.ebi.ac.uk/pdbsum/5v7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7e ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">e~~, ~~T4Tp126 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])~~<~~/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=5v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7e OCA], [~~http~~://pdbe.org/5v7e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v7e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v7e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7e ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Carlsson A-CC]]
-	[[Category: Carlsson, A ~~C.C]]~~	+
-	~~[[Category: Halogen bond]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein engineering]]~~	+
-	~~[[Category: T4 lysozyme]]~~	+
-	~~[[Category: Unnatural amino acid~~]]	+

OCA at 08:03, 27 November 2019

2019-11-27T08:03:11Z

←Older revision		Revision as of 08:03, 27 November 2019
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	==T4 lysozyme Y18Ymcl==		==T4 lysozyme Y18Ymcl==
-	<StructureSection load='5v7e' size='340' side='right' caption='[[5v7e]], [[Resolution\|resolution]] 1.36Å' scene=''>	+	<StructureSection load='5v7e' size='340' side='right'caption='[[5v7e]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v7e]] 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=5V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v7e]] 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=5V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7E FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5v7e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v7e" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Carlsson, A C.C]]		[[Category: Carlsson, A C.C]]

OCA at 07:32, 4 July 2018

2018-07-04T07:32:35Z

←Older revision		Revision as of 07:32, 4 July 2018
Line 3:		Line 3:
	<StructureSection load='5v7e' size='340' side='right' caption='[[5v7e]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='5v7e' size='340' side='right' caption='[[5v7e]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7e]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7e]] 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=5V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3CT:3-CHLORO-L-TYROSINE'>3CT</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3CT:3-CHLORO-L-TYROSINE'>3CT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v7d\|5v7d]], [[5v7f\|5v7f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v7d\|5v7d]], [[5v7f\|5v7f]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">e, T4Tp126 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=5v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7e OCA], [http://pdbe.org/5v7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7e RCSB], [http://www.ebi.ac.uk/pdbsum/5v7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7e ProSAT]</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=5v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7e OCA], [http://pdbe.org/5v7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7e RCSB], [http://www.ebi.ac.uk/pdbsum/5v7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7e ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The construction of more stable proteins is important in biomolecular engineering, particularly in the design of biologics-based therapeutics. We show here that replacing the tyrosine at position 18 (Y18) of T4 lysozyme with the unnatural amino acid m-chlorotyrosine ( (mCl)Y) increases both the thermal stability (increasing the melting temperature by approximately 1 degrees C and the melting enthalpy by 3 kcal/mol) and the enzymatic activity at elevated temperatures (15% higher than that of the parent enzyme at 40 degrees C) of this classic enzyme. The chlorine of (mCl)Y forms a halogen bond (XB) to the carbonyl oxygen of the peptide bond at glycine 28 (G28) in a tight loop near the active site. In this case, the XB potential of the typically weak XB donor Cl is shown from quantum chemical calculations to be significantly enhanced by polarization via an intramolecular hydrogen bond (HB) from the adjacent hydroxyl substituent of the tyrosyl side chain, resulting in a distinctive synergistic HB-enhanced XB (or HeX-B for short) interaction. The larger halogens (bromine and iodine) are not well accommodated within this same loop and, consequently, do not exhibit the effects on protein stability or function associated with the HeX-B interaction. Thus, we have for the first time demonstrated that an XB can be engineered to stabilize and increase the activity of an enzyme, with the increased stabilizing potential of the HeX-B further extending the application of halogenated amino acids in the design of more stable protein therapeutics.
		+
		+	Increasing Enzyme Stability and Activity through Hydrogen Bond-Enhanced Halogen Bonds.,Carlsson AC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS Biochemistry. 2018 Jul 3. doi: 10.1021/acs.biochem.8b00603. PMID:29921126<ref>PMID:29921126</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5v7e" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpt4]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Carlsson, A C.C]]		[[Category: Carlsson, A C.C]]

OCA at 05:39, 20 June 2018

2018-06-20T05:39:03Z

←Older revision		Revision as of 05:39, 20 June 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5v7e is ~~ON HOLD until Paper Publication~~	+	==T4 lysozyme Y18Ymcl==
-		+	<StructureSection load='5v7e' size='340' side='right' caption='[[5v7e]], [[Resolution\|resolution]] 1.36Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5v7e]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7E FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3CT:3-CHLORO-L-TYROSINE'>3CT</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v7d\|5v7d]], [[5v7f\|5v7f]]</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=5v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7e OCA], [http://pdbe.org/5v7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7e RCSB], [http://www.ebi.ac.uk/pdbsum/5v7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7e ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lysozyme]]
		+	[[Category: Carlsson, A C.C]]
		+	[[Category: Halogen bond]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protein engineering]]
		+	[[Category: T4 lysozyme]]
		+	[[Category: Unnatural amino acid]]

OCA at 09:42, 12 April 2017

2017-04-12T09:42:00Z

←Older revision		Revision as of 09:42, 12 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5v7e is ON HOLD	+	The entry 5v7e is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5v7e" [edit=sysop:move=sysop]

2017-04-05T11:41:24Z

Protected "5v7e" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:41, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v7e is ON HOLD Authors: Description: Category: Unreleased Structures

2017-04-05T11:41:23Z

New page: '''Unreleased structure''' The entry 5v7e is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5v7e is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]