1lyi: Difference between revisions

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-[[Image:1lyi.jpg|left|200px]]
- {{Structure
+==DISSECTION OF HELIX CAPPING IN T4 LYSOZYME BY STRUCTURAL AND THERMODYNAMIC ANALYSIS OF SIX AMINO ACID SUBSTITUTIONS AT THR 59==
-|PDB= 1lyi |SIZE=350|CAPTION= <scene name='initialview01'>1lyi</scene>, resolution 2.0&Aring;
+<StructureSection load='1lyi' size='340' side='right'caption='[[1lyi]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>
+<table><tr><td colspan='2'>[[1lyi]] 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=1LYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LYI FirstGlance]. <br>
-|ACTIVITY=
+</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&#8491;</td></tr>
-|GENE=
+<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=1lyi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lyi OCA], [https://pdbe.org/1lyi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lyi RCSB], [https://www.ebi.ac.uk/pdbsum/1lyi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lyi 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/ly/1lyi_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=1lyi ConSurf].
+<div style="clear:both"></div>
-'''DISSECTION OF HELIX CAPPING IN T4 LYSOZYME BY STRUCTURAL AND THERMODYNAMIC ANALYSIS OF SIX AMINO ACID SUBSTITUTIONS AT THR 59'''
+==See Also==
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==Overview==
+<references/>
-Threonine 59, a helix-capping residue at the amino terminus of the longest helix in T4 phage lysozyme, was substituted with valine, alanine, glycine, serine, asparagine, and aspartic acid. The valine, alanine, and glycine replacements were observed to be somewhat more destabilizing than serine, asparagine, and aspartic acid. The crystal structures of the different variants showed that changes in conformation occurred at the site of substitution, including Asp 61, which is nearby, as well as displacement of a solvent molecule that is hydrogen-bonded to the gamma-oxygen of Thr 59 in wild-type lysozyme. Neither the structures nor the stabilities of the mutant proteins support the hypothesis of Serrano and Fersht (1989) that glycine and alanine are better helix-capping residues than valine because a smaller-sized residue allows better hydration at the end of the helix. In the aspartic acid and asparagine replacements the substituted side chains form hydrogen bonds with the end of the helix, as does threonine and serine at this position. In contrast, however, the Asp and Asn side chains also make unusually close contacts with carbon atoms in Asp 61. This suggests a structural basis for the heretofore puzzling observations that asparagine is more frequently observed as a helix-capping residue than threonine [Richardson, J. S., &amp; Richardson, D. C. (1988) Science 240, 1648-1652] yet Thr----Asn replacements at N-cap positions in barnase were found to be destabilizing [Serrano, L., &amp; Fersht, A. R. (1989) Nature 342, 296-299].(ABSTRACT TRUNCATED AT 250 WORDS)
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia virus T4]]
-LYI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t2 Enterobacteria phage t2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LYI OCA].
+[[Category: Large Structures]]
+[[Category: Baase WA]]
-==Reference==
+[[Category: Becktel WJ]]
-Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59., Bell JA, Becktel WJ, Sauer U, Baase WA, Matthews BW, Biochemistry. 1992 Apr 14;31(14):3590-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1567817 1567817]
+[[Category: Bell JA]]
-[[Category: Enterobacteria phage t2]]
+[[Category: Matthews BW]]
-[[Category: Single protein]]
+[[Category: Sauer U]]
-[[Category: Baase, W A.]]
-[[Category: Becktel, W J.]]
-[[Category: Bell, J A.]]
-[[Category: Matthews, B W.]]
-[[Category: Sauer, U.]]
-[[Category: BME]]
-[[Category: CL]]
-[[Category: hydrolase(o-glycosyl)]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:36:40 2008''