244l: Difference between revisions

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New page: left|200px<br /><applet load="244l" size="450" color="white" frame="true" align="right" spinBox="true" caption="244l, resolution 1.7Å" /> '''THE RESPONSE OF T4 LY...
 
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[[Image:244l.jpg|left|200px]]<br /><applet load="244l" size="450" color="white" frame="true" align="right" spinBox="true"
caption="244l, resolution 1.7&Aring;" />
'''THE RESPONSE OF T4 LYSOZYME TO LARGE-TO-SMALL SUBSTITUTIONS WITHIN THE CORE AND ITS RELATION TO THE HYDROPHOBIC EFFECT'''<br />


==Overview==
==THE RESPONSE OF T4 LYSOZYME TO LARGE-TO-SMALL SUBSTITUTIONS WITHIN THE CORE AND ITS RELATION TO THE HYDROPHOBIC EFFECT==
To further examine the structural and thermodynamic basis of hydrophobic, stabilization in proteins, all of the bulky non-polar residues that are, buried or largely buried within the core of T4 lysozyme were substituted, with alanine. In 25 cases, including eight reported previously, it was, possible to determine the crystal structures of the variants. The, structures of four variants with double substitutions were also, determined. In the majority of cases the "large-to-small" substitutions, lead to internal cavities. In other cases declivities or channels open to, the surface were formed. In some cases the structural changes were minimal, (mainchain shifts &lt; or = 0.3 A); in other cases mainchain atoms moved up, to 2 A. In the case of Ile 29 --&gt; Ala the structure collapsed to such a, degree that the volume of the putative cavity was zero. Crystallographic, analysis suggests that the occupancy of the engineered cavities by solvent, is usually low. The mutants Val 149 --&gt; Ala (V149A) and Met 6 --&gt; Ala, (M6A), however, are exceptions and have, respectively, one and two, well-ordered water molecules within the cavity. The Val 149 --&gt; Ala, substitution allows the solvent molecule to hydrogen bond to polar atoms, that are occluded in the wild-type molecule. Similarly, the replacement of, Met 6 with alanine allows the two solvent molecules to hydrogen bond to, each other and to polar atoms on the protein. Except for Val 149 --&gt; Ala, the loss of stability of all the cavity mutants can be rationalized as a, combination of two terms. The first is a constant for a given class of, substitution (e.g., -2.1 kcal/mol for all Leu --&gt; Ala substitutions) and, can be considered as the difference between the free energy of transfer of, leucine and alanine from solvent to the core of the protein. The second, term can be considered as the energy cost of forming the cavity and is, consistent with a numerical value of 22 cal mol(-1) A(-3). Physically, this term is due to the loss of van der Waal's interactions between the, bulky sidechain that is removed and the atoms that form the wall of the, cavity. The overall results are consistent with the prior rationalization, of Leu --&gt; Ala mutants in T4 lysozyme by Eriksson et al. (Eriksson et al., 1992, Science 255:178-183).
<StructureSection load='244l' size='340' side='right'caption='[[244l]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[244l]] 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=244L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=244L 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]] 1.7&#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>, <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=244l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=244l OCA], [https://pdbe.org/244l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=244l RCSB], [https://www.ebi.ac.uk/pdbsum/244l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=244l 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/44/244l_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=244l ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
244L 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, BME 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=244L OCA].
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 
== References ==
==Reference==
<references/>
The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect., Xu J, Baase WA, Baldwin E, Matthews BW, Protein Sci. 1998 Jan;7(1):158-77. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9514271 9514271]
__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: Baldwin, E.]]
[[Category: Baldwin E]]
[[Category: Matthews, B.W.]]
[[Category: Matthews BW]]
[[Category: Xu, J.]]
[[Category: Xu J]]
[[Category: BME]]
[[Category: CL]]
[[Category: HED]]
[[Category: bacteriolytic enzyme]]
[[Category: glycosidase]]
[[Category: hydrolase]]
[[Category: o-glycosyl]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:49:12 2007''

Latest revision as of 12:09, 14 February 2024

THE RESPONSE OF T4 LYSOZYME TO LARGE-TO-SMALL SUBSTITUTIONS WITHIN THE CORE AND ITS RELATION TO THE HYDROPHOBIC EFFECTTHE RESPONSE OF T4 LYSOZYME TO LARGE-TO-SMALL SUBSTITUTIONS WITHIN THE CORE AND ITS RELATION TO THE HYDROPHOBIC EFFECT

Structural highlights

244l 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 1.7Å
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

244l, resolution 1.70Å

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