3a3r: Difference between revisions

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-{{Seed}}
-[[Image:3a3r.jpg|left|200px]]
-<!--
+==Structure of N59D HEN EGG-WHITE LYSOZYME==
-The line below this paragraph, containing "STRUCTURE_3a3r", creates the "Structure Box" on the page.
+<StructureSection load='3a3r' size='340' side='right'caption='[[3a3r]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3a3r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A3R FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</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=3a3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a3r OCA], [https://pdbe.org/3a3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a3r RCSB], [https://www.ebi.ac.uk/pdbsum/3a3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a3r ProSAT]</span></td></tr>
-{{STRUCTURE_3a3r|  PDB=3a3r  |  SCENE=  }}
+</table>
+== Function ==
+[https://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>
+== 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/a3/3a3r_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=3a3r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In the catalysis of sugar hydrolysis by hen egg-white lysozyme, Asp52 is thought to stabilize the reaction intermediate. This residue is involved in the well-ordered hydrogen bonding network including Asn46, Asp48, Ser50 and Asn59 on the anti-parallel beta-sheet, designated as a 'platform', on which the substrate sugar sits. To reveal the role of this hydrogen bonding network in the hydrolysis, we characterized Asn59 mutants by biochemical and crystallographic studies. Surprisingly, the introduction of only a methylene group by the Asn59Gln mutation markedly reduced the bacteriolytic activity and abolished the hydrolytic activity towards the synthetic substrate, PNP-(GlcNAc)(5). A similar result was also obtained with the Asn59Asp mutant. The crystal structure of the Asn59Asp mutant in complex with the substrate analogue revealed that, as in the wild-type, the (GlcNAc)(3) was bound in the A-B-C subsites. The reduced activity would be caused by subtle changes in the side-chain orientations as well as the electrostatic characteristics of Asp59, resulting in the rearrangement of the hydrogen bonding network of the platform. These results suggest that the precise locations of these 'platform' residues, maintained by the well-ordered hydrogen bonding network, are crucial for efficient hydrolysis.
-===Structure of N59D HEN EGG-WHITE LYSOZYME===
+Importance of the hydrogen bonding network including Asp52 for catalysis, as revealed by Asn59 mutant hen egg-white lysozymes.,Ose T, Kuroki K, Matsushima M, Maenaka K, Kumagai I J Biochem. 2009 Nov;146(5):651-7. Epub 2009 Jul 15. PMID:19605465<ref>PMID:19605465</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3a3r" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19605465}}, adds the Publication Abstract to the page
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19605465 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19605465}}
+__TOC__
+</StructureSection>
-==About this Structure==
-A3R is a 1 chain structure of 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=3A3R OCA].
-==Reference==
-<ref group="xtra">PMID:19605465</ref><references group="xtra"/>
 [[Category: Gallus gallus]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Kumagai, I.]]
+[[Category: Kumagai I]]
-[[Category: Kuroki, K.]]
+[[Category: Kuroki K]]
-[[Category: Maenaka, K.]]
+[[Category: Maenaka K]]
-[[Category: Matsushima, M.]]
+[[Category: Matsushima M]]
-[[Category: Ose, T.]]
+[[Category: Ose T]]
-[[Category: Allergen]]
-[[Category: Alpha and beta]]
-[[Category: Antimicrobial]]
-[[Category: Bacteriolytic enzyme]]
-[[Category: Disulfide bond]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov  4 10:53:37 2009''