252l

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(New page: 200px<br /><applet load="252l" size="450" color="white" frame="true" align="right" spinBox="true" caption="252l, resolution 2.1&Aring;" /> '''GENERATING LIGAND BIN...)
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[[Image:252l.jpg|left|200px]]<br /><applet load="252l" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="252l, resolution 2.1&Aring;" />
 
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'''GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS'''<br />
 
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==Overview==
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==GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS==
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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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<StructureSection load='252l' size='340' side='right'caption='[[252l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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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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</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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<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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==About this Structure==
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==See Also==
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252L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with CL and HED as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=252L OCA].
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
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== References ==
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==Reference==
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<references/>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=9514755 9514755]
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__TOC__
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[[Category: Bacteriophage t4]]
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</StructureSection>
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[[Category: Lysozyme]]
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[[Category: Escherichia virus T4]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Baase, W.A.]]
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[[Category: Baase WA]]
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[[Category: Baldwin, E.P.]]
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[[Category: Baldwin EP]]
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[[Category: Feher, V.]]
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[[Category: Feher V]]
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[[Category: Matthews, B.W.]]
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[[Category: Matthews BW]]
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[[Category: Zhang, X.J.]]
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[[Category: Zhang X-J]]
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[[Category: CL]]
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[[Category: HED]]
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[[Category: cavity mutants]]
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[[Category: hydrolase]]
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[[Category: ligand binding]]
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[[Category: multiple conformations]]
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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://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:49:48 2007''
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Current revision

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

PDB ID 252l

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