6syc: Difference between revisions
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==Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5== | ==Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5== | ||
<StructureSection load='6syc' size='340' side='right'caption='[[6syc]]' scene=''> | <StructureSection load='6syc' size='340' side='right'caption='[[6syc]], [[Resolution|resolution]] 1.38Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SYC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SYC FirstGlance]. <br> | <table><tr><td colspan='2'>[[6syc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SYC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SYC FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6syc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6syc OCA], [http://pdbe.org/6syc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6syc RCSB], [http://www.ebi.ac.uk/pdbsum/6syc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6syc ProSAT]</span></td></tr> | </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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=LYE:bromophenol+blue'>LYE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6syc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6syc OCA], [http://pdbe.org/6syc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6syc RCSB], [http://www.ebi.ac.uk/pdbsum/6syc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6syc ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Protein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein-dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme-bromophenol blue crystals: binding site I is located near the amino- and carboxyl-termini, while binding site II is located adjacent to helices alpha1 (residues 4-15) and alpha3 (residues 88-100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL-T1) show a single dye molecule bound to site II, and the crystals belong to space group P43212 without significant changes in the unit cell (a = b = 78.50, c = 37.34 A). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL-T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P212121) and unit cell (a = 38.00, b = 76.65, c = 84.86 A). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions. | |||
Lysozyme crystals dyed with bromophenol blue: where has the dye gone?,Plaza-Garrido M, Salinas-Garcia MC, Alba-Elena D, Martinez JC, Camara-Artigas A Acta Crystallogr D Struct Biol. 2020 Sep 1;76(Pt 9):845-856. doi:, 10.1107/S2059798320008803. Epub 2020 Sep 1. PMID:32876060<ref>PMID:32876060</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6syc" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Gallus gallus]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Camara-Artigas A]] | [[Category: Lysozyme]] | ||
[[Category: Plaza-Garrido M]] | [[Category: Camara-Artigas, A]] | ||
[[Category: Salinas-Garcia | [[Category: Plaza-Garrido, M]] | ||
[[Category: Salinas-Garcia, M C]] | |||
[[Category: Dye-soaking]] | |||
[[Category: Glycosidase]] | |||
[[Category: Hydrolase]] | |||
Revision as of 13:09, 16 September 2020
Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5Crystal structure of the lysozyme in presence of bromophenol blue at pH 6.5
Structural highlights
Function[LYSC_CHICK] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.[1] Publication Abstract from PubMedProtein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein-dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme-bromophenol blue crystals: binding site I is located near the amino- and carboxyl-termini, while binding site II is located adjacent to helices alpha1 (residues 4-15) and alpha3 (residues 88-100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL-T1) show a single dye molecule bound to site II, and the crystals belong to space group P43212 without significant changes in the unit cell (a = b = 78.50, c = 37.34 A). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL-T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P212121) and unit cell (a = 38.00, b = 76.65, c = 84.86 A). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions. Lysozyme crystals dyed with bromophenol blue: where has the dye gone?,Plaza-Garrido M, Salinas-Garcia MC, Alba-Elena D, Martinez JC, Camara-Artigas A Acta Crystallogr D Struct Biol. 2020 Sep 1;76(Pt 9):845-856. doi:, 10.1107/S2059798320008803. Epub 2020 Sep 1. PMID:32876060[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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