1qs5: Difference between revisions

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New page: left|200px<br /><applet load="1qs5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qs5, resolution 2.5Å" /> '''THE INTRODUCTION OF S...
 
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'''THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME'''<br />


==Overview==
==THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME==
In order to try to better understand the role played by strain in the, structure and stability of a protein a series of "small-to-large", mutations was made within the core of T4 lysozyme. Three different alanine, residues, one involved in backbone contacts, one in side-chain contacts, and the third adjacent to a small cavity, were each replaced with subsets, of the larger residues, Val, Leu, Ile, Met, Phe and Trp. As expected, the, protein is progressively destabilized as the size of the introduced, side-chain becomes larger. There does, however, seem to be a limit to the, destabilization, suggesting that a protein of a given size may be capable, of maintaining only a certain amount of strain. The changes in stability, vary greatly from site to site. Substitution of larger residues for both, Ala42 and Ala98 substantially destabilize the protein, even though the, primary contacts in one case are predominantly with side-chain atoms and, in the other with backbone. The results suggest that it is neither, practical nor meaningful to try to separate the effects of introduced, strain on side-chains from the effects on the backbone. Substitutions at, Ala129 are much less destabilizing than at sites 42 or 98. This is most, easily understood in terms of the pre-existing cavity, which provides, partial space to accommodate the introduced side-chains. Crystal, structures were obtained for a number of the mutants. These show that the, changes in structure to accommodate the introduced side-chains usually, consist of essentially rigid-body displacements of groups of linked atoms, achieved through relatively small changes in torsion angles. On rare, occasions, a side-chain close to the site of substitution may change to a, different rotamer. When such rotomer changes occur, they permit the, structure to dissipate strain by a response that is plastic rather than, elastic. In one case, a surface loop moves 1.2 A, not in direct response, to a mutation, but in an interaction mediated via an intermolecular, contact. It illustrates how the structure of a protein can be modified by, crystal contacts.
<StructureSection load='1qs5' size='340' side='right'caption='[[1qs5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1qs5]] 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=1QS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QS5 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]] 2.5&#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></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=1qs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qs5 OCA], [https://pdbe.org/1qs5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qs5 RCSB], [https://www.ebi.ac.uk/pdbsum/1qs5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qs5 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/qs/1qs5_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=1qs5 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1QS5 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 CL and HED 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=1QS5 OCA].
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 
== References ==
==Reference==
<references/>
The introduction of strain and its effects on the structure and stability of T4 lysozyme., Liu R, Baase WA, Matthews BW, J Mol Biol. 2000 Jan 7;295(1):127-45. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10623513 10623513]
__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: Liu, R.]]
[[Category: Liu R]]
[[Category: Matthews, B.W.]]
[[Category: Matthews BW]]
[[Category: CL]]
[[Category: HED]]
[[Category: mutant]]
[[Category: stability]]
[[Category: strain]]
[[Category: t4 lysozyme]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:56:15 2007''

Latest revision as of 11:16, 14 February 2024

THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYMETHE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME

Structural highlights

1qs5 is a 1 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Moussa SH, Kuznetsov V, Tran TA, Sacchettini JC, Young R. Protein determinants of phage T4 lysis inhibition. Protein Sci. 2012 Apr;21(4):571-82. doi: 10.1002/pro.2042. Epub 2012 Mar 2. PMID:22389108 doi:http://dx.doi.org/10.1002/pro.2042

1qs5, resolution 2.50Å

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