1d3n: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| (13 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
< | ==METHIONINE CORE MUTATION== | ||
<StructureSection load='1d3n' size='340' side='right'caption='[[1d3n]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
You may | == Structural highlights == | ||
or the | <table><tr><td colspan='2'>[[1d3n]] 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=1D3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3N 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]] 2Å</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1d3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3n OCA], [https://pdbe.org/1d3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3n RCSB], [https://www.ebi.ac.uk/pdbsum/1d3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3n 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/d3/1d3n_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1d3n ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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:10666571<ref>PMID:10666571</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1d3n" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Lysozyme 3D structures|Lysozyme 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Escherichia virus T4]] | ||
[[Category: Large Structures]] | |||
[[Category: Gassner NC]] | |||
== | [[Category: Matthews BW]] | ||
< | |||
[[Category: | |||
[[Category: | |||
[[Category: Gassner | |||
[[Category: Matthews | |||
Latest revision as of 09:31, 30 October 2024
METHIONINE CORE MUTATIONMETHIONINE CORE MUTATION
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] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedUsing 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. 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:10666571[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||