1rua: Difference between revisions

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-{{Seed}}
-[[Image:1rua.png|left|200px]]
-<!--
+==Crystal structure (B) of u.v.-irradiated cationic cyclization antibody 4C6 fab at pH 4.6 with a data set collected at SSRL beamline 11-1.==
-The line below this paragraph, containing "STRUCTURE_1rua", creates the "Structure Box" on the page.
+<StructureSection load='1rua' size='340' side='right'caption='[[1rua]], [[Resolution|resolution]] 1.75&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'>[[1rua]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RUA 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]] 1.75&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4HT:4-HYDROXYTRYPTOPHAN'>4HT</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=GHG:(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC+ACID+(NON-PREFERRED+NAME)'>GHG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-{{STRUCTURE_1rua|  PDB=1rua  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rua OCA], [https://pdbe.org/1rua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rua RCSB], [https://www.ebi.ac.uk/pdbsum/1rua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rua ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q58EU8_MOUSE Q58EU8_MOUSE]
+== 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/ru/1rua_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1rua ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Antibodies can catalyze the generation of hydrogen peroxide (H2O2) from singlet dioxygen (1O2*) and water via the postulated intermediacy of dihydrogen trioxide (H2O3) and other trioxygen species. Nine different crystal structures were determined to elucidate the chemical consequences to the antibody molecule itself of exposure to such reactive intermediates and to provide insights into the location on the antibody where these species could be generated. Herein, we report structural evidence for modifications of two specific antibody residues within the interfacial region of the variable and constant domains of different murine antibody antigen-binding fragments (Fabs) by reactive species generated during the antibody-catalyzed water oxidation process. Crystal structure analyses of murine Fabs 4C6 and 13G5 after UV-irradiation revealed complex oxidative modifications to tryptophan L163 and, in 4C6, hydroxylation of the Cgamma of glutamine H6. These discrete modifications of specific residues add further support for the "active site" of the water-oxidation pathway being located within the interfacial region of the constant and variable domains and highlight the general resistance of the antibody molecule to oxidation by reactive oxygen species generated during the water-oxidation process.
-===Crystal structure (B) of u.v.-irradiated cationic cyclization antibody 4C6 fab at pH 4.6 with a data set collected at SSRL beamline 11-1.===
+Probing the antibody-catalyzed water-oxidation pathway at atomic resolution.,Zhu X, Wentworth P Jr, Wentworth AD, Eschenmoser A, Lerner RA, Wilson IA Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2247-52. PMID:14982995<ref>PMID:14982995</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1rua" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14982995}}, adds the Publication Abstract to the page
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14982995 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14982995}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-RUA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RUA OCA].
-==Reference==
-Probing the antibody-catalyzed water-oxidation pathway at atomic resolution., Zhu X, Wentworth P Jr, Wentworth AD, Eschenmoser A, Lerner RA, Wilson IA, Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2247-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14982995 14982995]
-Structural basis for antibody catalysis of a cationic cyclization reaction., Zhu X, Heine A, Monnat F, Houk KN, Janda KD, Wilson IA, J Mol Biol. 2003 May 23;329(1):69-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12742019 12742019]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Eschenmoser A]]
-[[Category: Eschenmoser, A.]]
+[[Category: Lerner RA]]
-[[Category: Jr., P Wentworth.]]
+[[Category: Wentworth AD]]
-[[Category: Lerner, R A.]]
+[[Category: Wentworth Jr P]]
-[[Category: Wentworth, A D.]]
+[[Category: Wilson IA]]
-[[Category: Wilson, I A.]]
+[[Category: Zhu X]]
-[[Category: Zhu, X.]]
-[[Category: Amino acid modification]]
-[[Category: Catalytic antibody]]
-[[Category: Immunoglobulin]]
-[[Category: Water oxidation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 15:43:42 2008''