205l: Difference between revisions

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OCA

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-[[Image:205l.jpg|left|200px]]<br /><applet load="205l" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="205l, resolution 2.1&Aring;" />
-'''HOW AMINO-ACID INSERTIONS ARE ALLOWED IN AN ALPHA-HELIX OF T4 LYSOZYME'''<br />
-==Overview==
+==HOW AMINO-ACID INSERTIONS ARE ALLOWED IN AN ALPHA-HELIX OF T4 LYSOZYME==
-Studies of extant protein sequences indicate that amino-acid insertions, and deletions are preferentially located in loop regions, which has, traditionally been explained as the result of selection removing, deleterious mutations within secondary structural elements from the, population. But there is no a priori reason to discount the possibility, that insertions within secondary structure could either be tolerated until, compensatory mutations arise, or have effects that are propagated away, from secondary structure into loops. Earlier studies have indicated that, insertions are generally tolerated, although much less well within, secondary structure elements than in loop regions. Here we show that, amino-acid insertions in an alpha-helix of T4 lysozyme can be accepted in, two different ways. In some cases the inserted amino acids are, accommodated within the helix, leading to the translocation of wild-type, residues from the helix to the preceding loop. In other cases the, insertion causes a 'looping-out' in the first or last turn of the helix., The individual structural responses seem to be dominated by the, maintenance of the interface between the helix and the rest of the, protein.
+<StructureSection load='205l' size='340' side='right'caption='[[205l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[205l]] 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=205L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=205L 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]] 2.1&#8491;</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></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=205l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=205l OCA], [https://pdbe.org/205l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=205l RCSB], [https://www.ebi.ac.uk/pdbsum/205l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=205l 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/05/205l_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=205l ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t2 Enterobacteria phage t2] with CL and BME 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=205L OCA].
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-How amino-acid insertions are allowed in an alpha-helix of T4 lysozyme., Heinz DW, Baase WA, Dahlquist FW, Matthews BW, Nature. 1993 Feb 11;361(6412):561-4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8429913 8429913]
+__TOC__
-[[Category: Enterobacteria phage t2]]
+</StructureSection>
-[[Category: Lysozyme]]
+[[Category: Escherichia virus T4]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Heinz, D.W.]]
+[[Category: Heinz DW]]
-[[Category: Matthews, B.W.]]
+[[Category: Matthews BW]]
-[[Category: BME]]
-[[Category: CL]]
-[[Category: hydrolase(o-glycosyl)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:46:08 2007''