1d3f: Difference between revisions

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New page: left|200px<br /><applet load="1d3f" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d3f, resolution 2.05Å" /> '''N-TERMINAL DOMAIN CO...
 
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[[Image:1d3f.jpg|left|200px]]<br /><applet load="1d3f" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1d3f, resolution 2.05&Aring;" />
'''N-TERMINAL DOMAIN CORE METHIONINE MUTATION'''<br />


==Overview==
==N-TERMINAL DOMAIN CORE METHIONINE MUTATION==
Using heavily methionine-substituted T4 lysozyme as an example, it is, shown how the addition or deletion of a small number of methionines can, simplify the location of selenium sites for use in MAD phasing. By, comparing the X-ray data for a large number of singly substituted, lysozymes, it is shown that the optimal amino acid to be substituted by, methionine is leucine, followed, in order of preference, by phenylalanine, isoleucine and valine. The identification of leucine as the first choice, agrees with the ranking suggested by the Dayhoff mutation probability, i.e. by the frequency of amino-acid substitutions in the sequences of, related proteins. The ranking of the second and subsequent choices, however, differ significantly.
<StructureSection load='1d3f' size='340' side='right'caption='[[1d3f]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1d3f]] 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=1D3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3F 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]] 2.05&#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=1d3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3f OCA], [https://pdbe.org/1d3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3f RCSB], [https://www.ebi.ac.uk/pdbsum/1d3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3f 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/d3/1d3f_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=1d3f ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1D3F 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=1D3F OCA].
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 
== References ==
==Reference==
<references/>
Use of differentially substituted selenomethionine proteins in X-ray structure determination., Gassner NC, Matthews BW, Acta Crystallogr D Biol Crystallogr. 1999 Dec;55(Pt 12):1967-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10666571 10666571]
__TOC__
[[Category: Bacteriophage t4]]
</StructureSection>
[[Category: Lysozyme]]
[[Category: Escherichia virus T4]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Gassner, N.C.]]
[[Category: Gassner NC]]
[[Category: Matthews, B.W.]]
[[Category: Matthews BW]]
[[Category: CL]]
[[Category: HED]]
[[Category: hydrolase (o-glycosyl)]]
[[Category: methionine core mutant]]
[[Category: protein engineering]]
[[Category: protein folding]]
[[Category: t4 lysozyme]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:59:04 2007''

Latest revision as of 09:48, 7 February 2024

N-TERMINAL DOMAIN CORE METHIONINE MUTATIONN-TERMINAL DOMAIN CORE METHIONINE MUTATION

Structural highlights

1d3f 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 2.05Å
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

1d3f, resolution 2.05Å

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