3sb5: Difference between revisions

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<StructureSection load='3sb5' size='340' side='right'caption='[[3sb5]], [[Resolution|resolution]] 2.46&Aring;' scene=''>
<StructureSection load='3sb5' size='340' side='right'caption='[[3sb5]], [[Resolution|resolution]] 2.46&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3sb5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SB5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3sb5]] is a 4 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=3SB5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SB5 FirstGlance]. <br>
</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.46&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3sb6|3sb6]], [[3sb7|3sb7]], [[3sb8|3sb8]], [[3sb9|3sb9]], [[3sba|3sba]], [[3sbb|3sbb]]</div></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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">E ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></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=3sb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sb5 OCA], [https://pdbe.org/3sb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sb5 RCSB], [https://www.ebi.ac.uk/pdbsum/3sb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sb5 ProSAT]</span></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=3sb5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sb5 OCA], [https://pdbe.org/3sb5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sb5 RCSB], [https://www.ebi.ac.uk/pdbsum/3sb5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sb5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.  
[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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Combining the concepts of synthetic symmetrization with the approach of engineering metal binding sites, we have developed a new crystallization methodology termed metal-mediated synthetic symmetrization. In this method, pairs of histidine or cysteine mutations are introduced on the surface of target proteins, generating crystal lattice contacts or oligomeric assemblies upon coordination with metal. Metal-mediated synthetic symmetrization greatly expands the packing and oligomeric assembly possibilities of target proteins, thereby increasing the chances of growing diffraction-quality crystals. To demonstrate this method, we designed various T4 lysozyme (T4L) and maltose-binding protein (MBP) mutants and co-crystallized them with one of three metal ions: copper (Cu(2+) ), nickel (Ni(2+) ) or zinc (Zn(2+) ). The approach resulted in 16 new crystal structures - 8 for T4L and 8 for MBP - displaying a variety of oligomeric assemblies and packing modes, representing in total 13 new and distinct crystal forms for these proteins. We discuss the potential utility of the method for crystallizing target proteins of unknown structure by engineering in pairs of histidine or cysteine residues. As an alternate strategy, we propose that the varied crystallization-prone forms of T4L or MBP engineered in this work could be used as crystallization chaperones, by fusing them genetically to target proteins of interest.
 
An approach to crystallizing proteins by metal-mediated synthetic symmetrization.,Laganowsky A, Zhao M, Soriaga AB, Sawaya MR, Cascio D, Yeates TO Protein Sci. 2011 Sep 6. doi: 10.1002/pro.727. PMID:21898649<ref>PMID:21898649</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3sb5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bpt4]]
[[Category: Escherichia virus T4]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Lysozyme]]
[[Category: Cascio D]]
[[Category: Cascio, D]]
[[Category: Laganowsky A]]
[[Category: Laganowsky, A]]
[[Category: Sawaya MR]]
[[Category: Sawaya, M R]]
[[Category: Soriaga AB]]
[[Category: Soriaga, A B]]
[[Category: Yeates TO]]
[[Category: Yeates, T O]]
[[Category: Zhao M]]
[[Category: Zhao, M]]
[[Category: Hydrolase]]
[[Category: Metal-mediated synthetic symmetrization]]
[[Category: Synthetic symmetrization]]

Latest revision as of 12:48, 1 March 2024

Zn-mediated Trimer of T4 Lysozyme R125C/E128C by Synthetic SymmetrizationZn-mediated Trimer of T4 Lysozyme R125C/E128C by Synthetic Symmetrization

Structural highlights

3sb5 is a 4 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 2.46Å
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]

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

3sb5, resolution 2.46Å

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