1epy: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1epy.gif|left|200px]]<br /><applet load="1epy" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1epy, resolution 1.85&Aring;" />
-'''T4 LYSOZYME MUTANT, T21H/C54T/C97A/Q141H/T142H'''<br />
-==Overview==
+==T4 LYSOZYME MUTANT, T21H/C54T/C97A/Q141H/T142H==
-It is not easy to find candidate sites within a given protein where the, geometry of the polypeptide chain matches that of metal-binding sites in, known protein structures. By choosing a location in T4 lysozyme that is, inherently flexible, it was possible to engineer a two-histidine site that, binds different divalent cations. Crystallographic analysis shows that the, geometry of binding of zinc is distorted tetrahedral while that of cobalt, and nickel is octahedral. Insofar as spectroscopic data can be measured, they indicate that similar modes of coordination are retained in solution., The two substitutions, Thr21 --&gt; His and Thr142 --&gt; His, lie, respectively, on the surface of the N- and C-terminal domains on opposite, sides of the active site cleft. The design takes advantage of, hinge-bending motion which allows the binding site to adapt to the most, favorable ligand geometry for the metal. Introduction of the two, histidines increases the melting temperature of the protein by 2.0 degrees, C at pH 7.4. Metal binding further increases the melting temperature, but, only by a small amount (up to 1.5 degrees C). A third substitution, Gln141, --&gt; His, which could act as a third ligand in principle, does not do so, demonstrating the difficulty in mimicking naturally occurring, metal-binding sites.
+<StructureSection load='1epy' size='340' side='right'caption='[[1epy]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1epy]] 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=1EPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EPY 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=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1epy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1epy OCA], [https://pdbe.org/1epy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1epy RCSB], [https://www.ebi.ac.uk/pdbsum/1epy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1epy 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/ep/1epy_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=1epy ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-EPY 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 SO4, CL and CO 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=1EPY OCA].
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-Use of a non-rigid region in T4 lysozyme to design an adaptable metal-binding site., Wray JW, Baase WA, Ostheimer GJ, Zhang XJ, Matthews BW, Protein Eng. 2000 May;13(5):313-21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10835104 10835104]
+__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: Ostheimer, G.J.]]
+[[Category: Ostheimer GJ]]
-[[Category: Wray, J.W.]]
+[[Category: Wray JW]]
-[[Category: Zhang, X.J.]]
+[[Category: Zhang X-J]]
-[[Category: CL]]
-[[Category: CO]]
-[[Category: SO4]]
-[[Category: metal binding]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:13:03 2007''