2dqa: Difference between revisions

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-[[Image:2dqa.png|left|200px]]
-<!--
+==Crystal Structure of Tapes japonica Lysozyme==
-The line below this paragraph, containing "STRUCTURE_2dqa", creates the "Structure Box" on the page.
+<StructureSection load='2dqa' size='340' side='right'caption='[[2dqa]], [[Resolution|resolution]] 1.60&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'>[[2dqa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruditapes_philippinarum Ruditapes philippinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQA 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900017:triacetyl-beta-chitotriose'>PRD_900017</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
-{{STRUCTURE_2dqa|  PDB=2dqa  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqa OCA], [https://pdbe.org/2dqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dqa RCSB], [https://www.ebi.ac.uk/pdbsum/2dqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqa ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LYS_RUDPH LYS_RUDPH] Bacteriolytic activity against Gram-positive bacterium M.luteus and thereby probably protects against bacterial infection (PubMed:14523554, PubMed:15249048, PubMed:9914527). Also has chitinase activity (PubMed:14523554, PubMed:15249048, PubMed:17631496, PubMed:9914527). May act as an ispopeptidase, cleaving isopeptide bonds between the side chains of Lys and Gln residues in proteins or in the cross-linking peptide of peptidoglycan in bacterial cell walls (PubMed:14523554, PubMed:15249048).<ref>PMID:14523554</ref> <ref>PMID:15249048</ref> <ref>PMID:17631496</ref> <ref>PMID:9914527</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/dq/2dqa_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=2dqa ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tapes japonica lysozyme (TJL) is classified as a member of the recently established i-type lysozyme family. In this study, we solved the crystal structure of TJL complexed with a trimer of N-acetylglucosamine to 1.6A resolution. Based on structure and mutation analyses, we demonstrated that Glu-18 and Asp-30 are the catalytic residues of TJL. Furthermore, the present findings suggest that the catalytic mechanism of TJL is a retaining mechanism that proceeds through a covalent sugar-enzyme intermediate. On the other hand, the quaternary structure in the crystal revealed a dimer formed by the electrostatic interactions of catalytic residues (Glu-18 and Asp-30) in one molecule with the positive residues at the C terminus in helix 6 of the other molecule. Gel chromatography analysis revealed that the TJL dimer remained intact under low salt conditions but that it dissociated to TJL monomers under high salt conditions. With increasing salt concentrations, the chitinase activity of TJL dramatically increased. Therefore, this study provides novel evidence that the lysozyme activity of TJL is modulated by its quaternary structure.
-===Crystal Structure of Tapes japonica Lysozyme===
+Crystal structure of Tapes japonica Lysozyme with substrate analogue: structural basis of the catalytic mechanism and manifestation of its chitinase activity accompanied by quaternary structural change.,Goto T, Abe Y, Kakuta Y, Takeshita K, Imoto T, Ueda T J Biol Chem. 2007 Sep 14;282(37):27459-67. Epub 2007 Jul 13. PMID:17631496<ref>PMID:17631496</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2dqa" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17631496}}, adds the Publication Abstract to the page
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17631496 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17631496}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2dqa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Venerupis_philippinarum Venerupis philippinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQA OCA].
+[[Category: Ruditapes philippinarum]]
+[[Category: Abe Y]]
-==Reference==
+[[Category: Goto T]]
-<ref group="xtra">PMID:17631496</ref><references group="xtra"/>
+[[Category: Imoto T]]
-[[Category: Lysozyme]]
+[[Category: Kakuta Y]]
-[[Category: Venerupis philippinarum]]
+[[Category: Takeshita K]]
-[[Category: Abe, Y.]]
+[[Category: Ueda T]]
-[[Category: Goto, T.]]
-[[Category: Imoto, T.]]
-[[Category: Kakuta, Y.]]
-[[Category: Takeshita, K.]]
-[[Category: Ueda, T.]]