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==The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Structure with NAG to 1.7== | ==The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Structure with NAG to 1.7== | ||
<StructureSection load='3gxr' size='340' side='right' caption='[[3gxr]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='3gxr' size='340' side='right'caption='[[3gxr]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3gxr]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3gxr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atlantic_cod Atlantic cod]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GXR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GXR FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gxk|3gxk]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gxk|3gxk]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lysozyme ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lysozyme ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8049 Atlantic cod])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gxr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gxr OCA], [https://pdbe.org/3gxr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gxr RCSB], [https://www.ebi.ac.uk/pdbsum/3gxr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gxr ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
| Line 14: | Line 14: | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/3gxr_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/3gxr_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 37: | Line 37: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Atlantic cod]] | [[Category: Atlantic cod]] | ||
[[Category: Large Structures]] | |||
[[Category: Lysozyme]] | [[Category: Lysozyme]] | ||
[[Category: Finstad, S]] | [[Category: Finstad, S]] | ||
Revision as of 10:57, 16 March 2022
The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Structure with NAG to 1.7The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Structure with NAG to 1.7
Structural highlights
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 PubMedCrystal structures of Atlantic cod lysozyme have been solved with and without ligand bound in the active site to 1.7 and 1.9 A resolution, respectively. The structures reveal the presence of NAG in the substrate binding sites at both sides of the catalytic Glu73, hence allowing the first crystallographic description of the goose-type (g-type) lysozyme E-G binding sites. In addition, two aspartic acid residues suggested to participate in catalysis (Asp101 and Asp90) were mutated to alanine. Muramidase activity data for two single mutants and one double mutant demonstrates that both residues are involved in catalysis, but Asp101 is the more critical of the two. The structures and activity data suggest that a water molecule is the nucleophile completing the catalytic reaction, and the roles of the aspartic acids are to ensure proper positioning of the catalytic water. Crystal structures of g-type lysozyme from Atlantic cod shed new light on substrate binding and the catalytic mechanism.,Helland R, Larsen RL, Finstad S, Kyomuhendo P, Larsen AN Cell Mol Life Sci. 2009 Aug;66(15):2585-98. Epub 2009 Jun 20. PMID:19543850[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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