2f47: Difference between revisions

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-[[Image:2f47.png|left|200px]]
-<!--
+==Xray crystal structure of T4 lysozyme mutant L20/R63A liganded to methylguanidinium==
-The line below this paragraph, containing "STRUCTURE_2f47", creates the "Structure Box" on the page.
+<StructureSection load='2f47' size='340' side='right'caption='[[2f47]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2f47]] 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=2F47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F47 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</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>, <scene name='pdbligand=MGX:1-METHYLGUANIDINE'>MGX</scene></td></tr>
-{{STRUCTURE_2f47|  PDB=2f47  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f47 OCA], [https://pdbe.org/2f47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f47 RCSB], [https://www.ebi.ac.uk/pdbsum/2f47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f47 ProSAT]</span></td></tr>
+</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>
+== 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/f4/2f47_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/main_output.php?pdb_ID=2f47 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The binding of guanidinium ion has been shown to promote a large-scale translation of a tandemly duplicated helix in an engineered mutant of T4 lysozyme. The guanidinium ion acts as a surrogate for the guanidino group of an arginine side chain. Here we determine whether methyl- and ethylguanidinium provide better mimics. The results show that addition of the hydrophobic moieties to the ligand enhances the binding affinity concomitant with reduction in ligand solubility. Crystallographic analysis confirms that binding of the alternative ligands to the engineered site still drives the large-scale conformational change. Thermal analysis and NMR data show, in comparison to guanidinium, an increase in protein stability and in ligand affinity. This is presumably due to the successive increase in hydrophobicity in going from guanidinium to ethylguanidinium. A fluorescence-based optical method was developed to sense the ligand-triggered helix translation in solution. The results are a first step in the de novo design of a molecular switch that is not related to the normal function of the protein.
-===Xray crystal structure of T4 lysozyme mutant L20/R63A liganded to methylguanidinium===
+Guanidinium derivatives bind preferentially and trigger long-distance conformational changes in an engineered T4 lysozyme.,Yousef MS, Bischoff N, Dyer CM, Baase WA, Matthews BW Protein Sci. 2006 Apr;15(4):853-61. PMID:16600969<ref>PMID:16600969</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2f47" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16600969}}, adds the Publication Abstract to the page
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16600969 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16600969}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia virus T4]]
-[[2f47]] 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=2F47 OCA].
+[[Category: Large Structures]]
+[[Category: Baase WA]]
-==Reference==
+[[Category: Bischoff N]]
-<ref group="xtra">PMID:16600969</ref><ref group="xtra">PMID:15286283</ref><ref group="xtra">PMID:10339544</ref><ref group="xtra">PMID:12869697</ref><references group="xtra"/>
+[[Category: Dyer CM]]
-[[Category: Enterobacteria phage t4]]
+[[Category: Matthews BW]]
-[[Category: Lysozyme]]
+[[Category: Yousef MS]]
-[[Category: Baase, W A.]]
-[[Category: Bischoff, N.]]
-[[Category: Dyer, C M.]]
-[[Category: Matthews, B W.]]
-[[Category: Yousef, M S.]]
-[[Category: Hydrolase]]
-[[Category: Molecular switch]]
-[[Category: Nano-bitechnology]]
-[[Category: Protein design]]
-[[Category: Protein engineering]]
-[[Category: T4 lysozyme]]