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2dqa

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[[Image:2dqa.jpg|left|200px]]
 
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{{Structure
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==Crystal Structure of Tapes japonica Lysozyme==
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|PDB= 2dqa |SIZE=350|CAPTION= <scene name='initialview01'>2dqa</scene>, resolution 1.60&Aring;
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<StructureSection load='2dqa' size='340' side='right'caption='[[2dqa]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>
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<table><tr><td colspan='2'>[[2dqa]] is a 2 chain structure. 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>
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|ACTIVITY= <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>
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</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=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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|GENE=
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<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>
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|DOMAIN=
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<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>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqa OCA], [http://www.ebi.ac.uk/pdbsum/2dqa PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dqa RCSB]</span>
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== Evolutionary Conservation ==
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}}
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dq/2dqa_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal Structure of Tapes japonica Lysozyme'''
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2dqa" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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.
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2DQA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Tapes_japonica Tapes japonica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQA OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17631496 17631496]
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[[Category: Lysozyme]]
[[Category: Lysozyme]]
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[[Category: Single protein]]
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[[Category: Abe, Y]]
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[[Category: Tapes japonica]]
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[[Category: Goto, T]]
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[[Category: Abe, Y.]]
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[[Category: Imoto, T]]
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[[Category: Goto, T.]]
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[[Category: Kakuta, Y]]
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[[Category: Imoto, T.]]
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[[Category: Takeshita, K]]
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[[Category: Kakuta, Y.]]
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[[Category: Ueda, T]]
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[[Category: Takeshita, K.]]
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[[Category: Enzyme]]
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[[Category: Ueda, T.]]
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[[Category: Hydrolase]]
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[[Category: enzyme]]
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[[Category: Substrate complex]]
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[[Category: hydrolase]]
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[[Category: lysozyme]]
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[[Category: substrate complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:38:00 2008''
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Current revision

Crystal Structure of Tapes japonica Lysozyme

PDB ID 2dqa

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