1g06: Difference between revisions

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-[[Image:1g06.gif|left|200px]]<br /><applet load="1g06" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1g06, resolution 1.85&Aring;" />
-'''CRYSTAL STRUCTURE OF T4 LYSOZYME MUTANT V149S'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF T4 LYSOZYME MUTANT V149S==
-To investigate the structural and thermodynamic basis of the binding of, solvent at internal sites within proteins a number of mutations were, constructed in T4 lysozyme. Some of these were designed to introduce new, solvent-binding sites. Others were intended to displace solvent from, preexisting sites. In one case Val-149 was replaced with alanine, serine, cysteine, threonine, isoleucine, and glycine. Crystallographic analysis, shows that, with the exception of isoleucine, each of these substitutions, results in the binding of solvent at a polar site that is sterically, blocked in the wild-type enzyme. Mutations designed to perturb or displace, a solvent molecule present in the native enzyme included the replacement, of Thr-152 with alanine, serine, cysteine, valine, and isoleucine., Although the solvent molecule was moved in some cases by up to 1.7 A, in, no case was it completely removed from the folded protein. The results, suggest that hydrogen bonds from the protein to bound solvent are energy, neutral. The binding of solvent to internal sites within proteins also, appears to be energy neutral except insofar as the bound solvent may, prevent a loss of energy due to potential hydrogen bonding groups that, would otherwise be unsatisfied. The introduction of a solvent-binding site, appears to require not only a cavity to accommodate the water molecule but, also the presence of polar groups to help satisfy its hydrogen-bonding, potential. It may be easier to design a site to accommodate two or more, water molecules rather than one as the solvent molecules can then, hydrogen-bond to each other. For similar reasons it is often difficult to, design a point mutation that will displace a single solvent molecule from, the core of a protein.
+<StructureSection load='1g06' size='340' side='right'caption='[[1g06]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1g06]] 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=1G06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G06 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
+<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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g06 OCA], [https://pdbe.org/1g06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g06 RCSB], [https://www.ebi.ac.uk/pdbsum/1g06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g06 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/g0/1g06_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=1g06 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-G06 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=1G06 OCA].
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme., Xu J, Baase WA, Quillin ML, Baldwin EP, Matthews BW, Protein Sci. 2001 May;10(5):1067-78. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11316887 11316887]
+__TOC__
-[[Category: Bacteriophage t4]]
+</StructureSection>
-[[Category: Lysozyme]]
+[[Category: Escherichia virus T4]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Baase, W.A.]]
+[[Category: Baase WA]]
-[[Category: Matthews, B.W.]]
+[[Category: Matthews BW]]
-[[Category: Quillin, M.L.]]
+[[Category: Quillin ML]]
-[[Category: Xu, J.]]
+[[Category: Xu J]]
-[[Category: CL]]
-[[Category: HED]]
-[[Category: bacteriolytic enzyme]]
-[[Category: glycosidase]]
-[[Category: hydrolase]]
-[[Category: o-glycosyl]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:34:34 2007''