252l

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[[Image:252l.jpg|left|200px]]
 
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==GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS==
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The line below this paragraph, containing "STRUCTURE_252l", creates the "Structure Box" on the page.
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<StructureSection load='252l' size='340' side='right'caption='[[252l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[252l]] 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=252L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=252L FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene></td></tr>
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{{STRUCTURE_252l| PDB=252l | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=252l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=252l OCA], [https://pdbe.org/252l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=252l RCSB], [https://www.ebi.ac.uk/pdbsum/252l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=252l ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/52/252l_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=252l ConSurf].
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<div style="clear:both"></div>
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'''GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS'''
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==See Also==
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
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== References ==
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==Overview==
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<references/>
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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.
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia virus T4]]
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252L is a [[Single protein]] structure of 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=252L OCA].
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[[Category: Large Structures]]
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[[Category: Baase WA]]
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==Reference==
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[[Category: Baldwin EP]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/9514755 9514755]
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[[Category: Feher V]]
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[[Category: Enterobacteria phage t4]]
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[[Category: Matthews BW]]
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[[Category: Lysozyme]]
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[[Category: Zhang X-J]]
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[[Category: Single protein]]
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[[Category: Baase, W A.]]
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[[Category: Baldwin, E P.]]
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[[Category: Feher, V.]]
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[[Category: Matthews, B W.]]
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[[Category: Zhang, X J.]]
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[[Category: Cavity mutant]]
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[[Category: Hydrolase]]
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[[Category: Ligand binding]]
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[[Category: Multiple conformation]]
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[[Category: O-glycosyl]]
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[[Category: Protein design]]
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[[Category: Protein engineering]]
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[[Category: T4 lysozyme]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:23:22 2008''
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Current revision

GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS

PDB ID 252l

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