229l: Difference between revisions

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 ==GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS==
-<StructureSection load='229l' size='340' side='right' caption='[[229l]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='229l' size='340' side='right'caption='[[229l]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[229l]] 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=229L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=229L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[229l]] 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=229L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=229L 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>, <scene name='pdbligand=GAI:GUANIDINE'>GAI</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]] 1.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GENE E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=GAI:GUANIDINE'>GAI</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=229l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=229l OCA], [https://pdbe.org/229l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=229l RCSB], [https://www.ebi.ac.uk/pdbsum/229l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=229l 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=229l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=229l OCA], [http://pdbe.org/229l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=229l RCSB], [http://www.ebi.ac.uk/pdbsum/229l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=229l ProSAT]</span></td></tr>
 </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.
+[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]]
@@ Line 21: / 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=229l ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Several variants of T4 lysozyme have been identified that sequester small organic ligands in cavities or clefts. To evaluate potential binding sites for non-polar molecules, we screened a number of hydrophobic large-to-small mutants for stabilization in the presence of benzene. In addition to Leu99--&gt;Ala, binding was indicated for at least five other mutants. Variants Met102--&gt;Ala and Leu133--&gt;Gly, and a crevice mutant, Phe104--&gt;Ala, were further characterized using X-ray crystallography and thermal denaturation. As predicted from the shape of the cavity in the benzene complex, mutant Leu133--&gt;Gly also bound p-xylene. We attempted to enlarge the cavity of the Met102--&gt;Ala mutant into a deep crevice through an additional substitution, but the double mutant failed to bind ligands because an adjacent helix rearranged into a non-helical structure, apparently due to the loss of packing interactions. In general, the protein structure contracted slightly to reduce the volume of the void created by truncating substitutions and expanded upon binding the non-polar ligand, with shifts similar to those resulting from the mutations.A polar molecule binding site was also created by truncating Arg95 to alanine. This creates a highly complementary buried polar environment that can be utilized as a specific "receptor" for a guanidinium ion. Our results suggest that creating a deficiency through truncating mutations of buried residues generates "binding potential" for ligands with characteristics similar to the deleted side-chain. Analysis of complex and apo crystal structures of binding and non-binding mutants suggests that ligand size and shape as well as protein flexibility and complementarity are all determinants of binding. Binding at non-polar sites is governed by hydrophobicity and steric interactions and is relatively permissive. Binding at a polar site is more restrictive and requires extensive complementarity between the ligand and the site.
-Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions.,Baldwin E, Baase WA, Zhang X, Feher V, Matthews BW J Mol Biol. 1998 Mar 27;277(2):467-85. PMID:9514755<ref>PMID:9514755</ref>
+==See Also==
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 229l" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bpt4]]
+[[Category: Escherichia virus T4]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Baase, W A]]
+[[Category: Baase WA]]
-[[Category: Baldwin, E P]]
+[[Category: Baldwin EP]]
-[[Category: Feher, V]]
+[[Category: Feher V]]
-[[Category: Matthews, B W]]
+[[Category: Matthews BW]]
-[[Category: Zhang, X J]]
+[[Category: Zhang X-J]]
-[[Category: Cavity mutant]]
-[[Category: Hydrolase]]
-[[Category: Ligand binding]]
-[[Category: O-glycosyl]]
-[[Category: Protein design]]
-[[Category: Protein engineering]]
-[[Category: T4 lysozyme]]