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[[Image:1dyc.gif|left|200px]]<br /><applet load="1dyc" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1dyc, resolution 2.1&Aring;" />
'''DETERMINATION OF ALPHA-HELIX PROPENSITY WITHIN THE CONTEXT OF A FOLDED PROTEIN: SITES 44 AND 131 IN BACTERIOPHAGE T4 LYSOZYME'''<br />


==Overview==
==DETERMINATION OF ALPHA-HELIX PROPENSITY WITHIN THE CONTEXT OF A FOLDED PROTEIN: SITES 44 AND 131 IN BACTERIOPHAGE T4 LYSOZYME==
To determine the effects of different amino acids on the structure and stability of an alpha-helix in the context of a globular protein, all 19 naturally-occurring amino acids were substituted for Ser44 in phage T4 lysozyme. A more restricted set of nine replacements was also made for Val131. Ser44 and Val131 are two of a very limited number of possible sites in T4 lysozyme that are well within alpha-helices, are solvent-exposed and relatively free of interactions with neighboring residues, and are not involved in crystal contacts. High resolution structures for the majority of the mutants, some of which crystallized non-isomorphously with wild-type, were determined. With the exception of proline, the amino acid substitutions caused little if any perturbation of the alpha-helix backbone. Also the beta-branched residues Thr, Val and Ile show no indication of either side-chain or backbone distortion. Therefore, other than proline, there is no evidence that differences in helix propensities are associated with different amounts of strain introduced into the helix. For reference, and also to allow estimates of side-chain entropy, a survey was made of side-chain conformations in 100 well-refined protein structures. As noted previously all side-chains within alpha-helices strongly avoid the g- conformation (chi 1 approximately 60 degrees). This restricts the beta-branched residues Thr, Val and Ile to a single conformer (g+, chi 1 approximately -60 degrees). Asp, Asn, Met and Ser within helices also overwhelmingly prefer the g+ conformation. For Arg, Cys, Gln, Glu, Leu and Lys the t (chi 1 approximately 180 degrees) and g+ conformers are populated roughly equally. Only the aromatic residues, His, Tyr, Trp and Phe prefer the t conformation. These preferences are the same whether the side-chain is buried or solvent-exposed. In general, the side-chain conformations adopted by the residues substituted at positions 44 and 131 correspond to the most commonly observed conformation for the same amino acid in helices in known protein structures. The changes in protein stability for the replacements at site 131 in general agree well with those at site 44 (correlation r = 0.97), suggesting that these may be representative of substitutions at fully solvent-exposed sites in the middle of alpha-helices. The free energy values also agree quite well with those observed for equivalent replacements in a number of soluble alpha-helical model peptides and with data from "host-guest" studies and statistical surveys (r = 0.69 to 0.93).(ABSTRACT TRUNCATED AT 400 WORDS)
<StructureSection load='1dyc' size='340' side='right'caption='[[1dyc]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1dyc]] 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=1DYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DYC 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]] 2.1&#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></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=1dyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dyc OCA], [https://pdbe.org/1dyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dyc RCSB], [https://www.ebi.ac.uk/pdbsum/1dyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dyc 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/dy/1dyc_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=1dyc ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1DYC 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 <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=BME:'>BME</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1DYC OCA].
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 
== References ==
==Reference==
<references/>
Determination of alpha-helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme., Blaber M, Zhang XJ, Lindstrom JD, Pepiot SD, Baase WA, Matthews BW, J Mol Biol. 1994 Jan 14;235(2):600-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8289284 8289284]
__TOC__
[[Category: Bacteriophage t4]]
</StructureSection>
[[Category: Lysozyme]]
[[Category: Escherichia virus T4]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Matthews, B W.]]
[[Category: Matthews BW]]
[[Category: Zhang, X.]]
[[Category: Zhang X]]
[[Category: BME]]
[[Category: CL]]
[[Category: hydrolase(o-glycosyl)]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:21:48 2008''

Latest revision as of 10:00, 7 February 2024

DETERMINATION OF ALPHA-HELIX PROPENSITY WITHIN THE CONTEXT OF A FOLDED PROTEIN: SITES 44 AND 131 IN BACTERIOPHAGE T4 LYSOZYMEDETERMINATION OF ALPHA-HELIX PROPENSITY WITHIN THE CONTEXT OF A FOLDED PROTEIN: SITES 44 AND 131 IN BACTERIOPHAGE T4 LYSOZYME

Structural highlights

1dyc 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 2.1Å
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

1dyc, resolution 2.10Å

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