1p6y: Difference between revisions

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-[[Image:1p6y.png|left|200px]]
-{{STRUCTURE_1p6y|  PDB=1p6y  |  SCENE=  }}
+==T4 LYSOZYME CORE REPACKING MUTANT M120Y/TA==
+<StructureSection load='1p6y' size='340' side='right'caption='[[1p6y]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1p6y]] 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=1P6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P6Y 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]] 1.54&#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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1p6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p6y OCA], [https://pdbe.org/1p6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p6y RCSB], [https://www.ebi.ac.uk/pdbsum/1p6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p6y 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/p6/1p6y_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=1p6y ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Automated protein redesign, as implemented in the program ORBIT, was used to redesign the core of phage T4 lysozyme. A total of 26 buried or partially buried sites in the C-terminal domain were allowed to vary both their sequence and side-chain conformation while the backbone and non-selected side-chains remained fixed. A variant with seven substitutions ("Core-7") was identified as having the most favorable energy. The redesign experiment was repeated with a penalty for the presence of methionine residues. In this case the redesigned protein ("Core-10") had ten amino acid changes. The two designed proteins, as well as the constituent single mutants, and several single-site revertants were over-expressed in Escherichia coli, purified, and subjected to crystallographic and thermal analyses. The thermodynamic and structural data show that some repacking was achieved although neither redesigned protein was more stable than the wild-type protein. The use of the methionine penalty was shown to be effective. Several of the side-chain rotamers in the predicted structure of Core-10 differ from those observed. Rather than changing to new rotamers predicted by the design process, side-chains tend to maintain conformations similar to those seen in the native molecule. In contrast, parts of the backbone change by up to 2.8A relative to both the designed structure and wild-type.Water molecules that are present within the lysozyme molecule were removed during the design process. In the redesigned protein the resultant cavities were, to some degree, re-occupied by side-chain atoms. In the observed structure, however, water molecules were still bound at or near their original sites. This suggests that it may be preferable to leave such water molecules in place during the design procedure. The results emphasize the specificity of the packing that occurs within the core of a typical protein. While point substitutions within the core are tolerated they almost always result in a loss of stability. Likewise, combinations of substitutions may also be tolerated but usually destabilize the protein. Experience with T4 lysozyme suggests that a general core repacking methodology with retention or enhancement of stability may be difficult to achieve without provision for shifts in the backbone.
-===T4 LYSOZYME CORE REPACKING MUTANT M120Y/TA===
+Repacking the Core of T4 lysozyme by automated design.,Mooers BH, Datta D, Baase WA, Zollars ES, Mayo SL, Matthews BW J Mol Biol. 2003 Sep 19;332(3):741-56. PMID:12963380<ref>PMID:12963380</ref>
-{{ABSTRACT_PUBMED_12963380}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1p6y" style="background-color:#fffaf0;"></div>
-[[1p6y]] is a 1 chain structure of [[Hen Egg-White (HEW) Lysozyme]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P6Y OCA].
 ==See Also==
-*[[Hen Egg-White (HEW) Lysozyme|Hen Egg-White (HEW) Lysozyme]]
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:012963380</ref><references group="xtra"/>
+__TOC__
-[[Category: Enterobacteria phage t4]]
+</StructureSection>
-[[Category: Lysozyme]]
+[[Category: Escherichia virus T4]]
-[[Category: Baase, W A.]]
+[[Category: Large Structures]]
-[[Category: Datta, D.]]
+[[Category: Baase WA]]
-[[Category: Matthews, B W.]]
+[[Category: Datta D]]
-[[Category: Mayo, S L.]]
+[[Category: Matthews BW]]
-[[Category: Mooers, B H.]]
+[[Category: Mayo SL]]
-[[Category: Zollars, E S.]]
+[[Category: Mooers BH]]
-[[Category: Automated protein design]]
+[[Category: Zollars ES]]
-[[Category: Back revertant]]
-[[Category: Core repacking]]
-[[Category: Dead-end elimination theorem]]
-[[Category: Designed core mutant]]
-[[Category: Hydrolase]]
-[[Category: Optimized rotamer combination]]
-[[Category: Orbit]]
-[[Category: Protein engineering]]
-[[Category: Protein folding]]
-[[Category: Protein stability]]
-[[Category: Side-chain packing]]
-[[Category: T4 lysozyme]]