4w54: Difference between revisions
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==T4 Lysozyme L99A with Ethylbenzene Bound== | ==T4 Lysozyme L99A with Ethylbenzene Bound== | ||
<StructureSection load='4w54' size='340' side='right' caption='[[4w54]], [[Resolution|resolution]] 1.79Å' scene=''> | <StructureSection load='4w54' size='340' side='right'caption='[[4w54]], [[Resolution|resolution]] 1.79Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4w54]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4w54]] 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=4W54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W54 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7901Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PYJ:PHENYLETHANE'>PYJ</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4w54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w54 OCA], [https://pdbe.org/4w54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w54 RCSB], [https://www.ebi.ac.uk/pdbsum/4w54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w54 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == 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> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 4w54" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 4w54" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Lysin 3D structures|Lysin 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia virus T4]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Eidam | [[Category: Eidam O]] | ||
[[Category: Fischer | [[Category: Fischer M]] | ||
[[Category: Merski | [[Category: Merski M]] | ||
[[Category: Shoichet | [[Category: Shoichet BK]] | ||
Latest revision as of 10:27, 27 September 2023
T4 Lysozyme L99A with Ethylbenzene BoundT4 Lysozyme L99A with Ethylbenzene Bound
Structural highlights
FunctionENLYS_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.[1] Publication Abstract from PubMedConformational change in protein-ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few substantial series of congeneric ligand complexes in the Protein Data Bank (PDB). Here we determine the structures of eight alkyl benzenes, in single-methylene increases from benzene to n-hexylbenzene, bound to an enclosed cavity in T4 lysozyme. The volume of the apo cavity suffices to accommodate benzene but, even with toluene, larger cavity conformations become observable in the electron density, and over the series two other major conformations are observed. These involve discrete changes in main-chain conformation, expanding the site; few continuous changes in the site are observed. In most structures, two discrete protein conformations are observed simultaneously, and energetic considerations suggest that these conformations are low in energy relative to the ground state. An analysis of 121 lysozyme cavity structures in the PDB finds that these three conformations dominate the previously determined structures, largely modeled in a single conformation. An investigation of the few congeneric series in the PDB suggests that discrete changes are common adaptations to a series of growing ligands. The discrete, but relatively few, conformational states observed here, and their energetic accessibility, may have implications for anticipating protein conformational change in ligand design. Homologous ligands accommodated by discrete conformations of a buried cavity.,Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK Proc Natl Acad Sci U S A. 2015 Apr 6. pii: 201500806. PMID:25847998[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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