1ibd: Difference between revisions

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-[[Image:1ibd.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1ibd", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_1ibd|  PDB=1ibd  |  SCENE=  }}
-'''X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29A'''
+==X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29A==
+<StructureSection load='1ibd' size='340' side='right'caption='[[1ibd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ibd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Photobacterium_leiognathi_subsp._leiognathi Photobacterium leiognathi subsp. leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IBD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1ibd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibd OCA], [https://pdbe.org/1ibd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ibd RCSB], [https://www.ebi.ac.uk/pdbsum/1ibd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
+== 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/ib/1ibd_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=1ibd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The functional properties and X-ray structures of five mutant forms of Photobacterium leiognathi Cu,Zn superoxide dismutase carrying single mutations at residues located at the dimer association interface have been investigated. When compared to the wild-type enzyme, the three-dimensional structures of the mutants show structural perturbations limited to the proximity of the mutation sites and substantial identity of active site geometry. Nonetheless, the catalytic rates of all mutants, measured at neutral pH and low ionic strength by pulse radiolysis, are higher than that of the wild-type protein. Such enzymatic activity increase is paralleled by enhanced active site accessibility to external chelating agents, which, in the mutated enzyme, remove more readily the active site copper ion. It is concluded that mutations at the prokaryotic Cu,Zn superoxide dismutase subunit interface can transduce dynamical perturbation to the active site region, promoting substrate active site accessibility. Such long-range intramolecular communication effects have not been extensively described before within the Cu,Zn superoxide dismutase homology family.
-==Overview==
+Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase.,Stroppolo ME, Pesce A, D'Orazio M, O'Neill P, Bordo D, Rosano C, Milani M, Battistoni A, Bolognesi M, Desideri A J Mol Biol. 2001 May 4;308(3):555-63. PMID:11327787<ref>PMID:11327787</ref>
-The functional properties and X-ray structures of five mutant forms of Photobacterium leiognathi Cu,Zn superoxide dismutase carrying single mutations at residues located at the dimer association interface have been investigated. When compared to the wild-type enzyme, the three-dimensional structures of the mutants show structural perturbations limited to the proximity of the mutation sites and substantial identity of active site geometry. Nonetheless, the catalytic rates of all mutants, measured at neutral pH and low ionic strength by pulse radiolysis, are higher than that of the wild-type protein. Such enzymatic activity increase is paralleled by enhanced active site accessibility to external chelating agents, which, in the mutated enzyme, remove more readily the active site copper ion. It is concluded that mutations at the prokaryotic Cu,Zn superoxide dismutase subunit interface can transduce dynamical perturbation to the active site region, promoting substrate active site accessibility. Such long-range intramolecular communication effects have not been extensively described before within the Cu,Zn superoxide dismutase homology family.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-IBD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBD OCA].
+</div>
+<div class="pdbe-citations 1ibd" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase., Stroppolo ME, Pesce A, D'Orazio M, O'Neill P, Bordo D, Rosano C, Milani M, Battistoni A, Bolognesi M, Desideri A, J Mol Biol. 2001 May 4;308(3):555-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11327787 11327787]
+*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
-[[Category: Photobacterium leiognathi]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Superoxide dismutase]]
+__TOC__
-[[Category: Battistoni, A.]]
+</StructureSection>
-[[Category: Bolognesi, M.]]
+[[Category: Large Structures]]
-[[Category: Bordo, D.]]
+[[Category: Photobacterium leiognathi subsp. leiognathi]]
-[[Category: Desideri, A.]]
+[[Category: Battistoni A]]
-[[Category: Milani, M.]]
+[[Category: Bolognesi M]]
-[[Category: Neill, P O.]]
+[[Category: Bordo D]]
-[[Category: Orazio, M D.]]
+[[Category: D'Orazio M]]
-[[Category: Pesce, A.]]
+[[Category: Desideri A]]
-[[Category: Rosano, C.]]
+[[Category: Milani M]]
-[[Category: Stroppolo, M E.]]
+[[Category: O'Neill P]]
-[[Category: Prokaryotic superoxide dismutase]]
+[[Category: Pesce A]]
-[[Category: Subunit interaction]]
+[[Category: Rosano C]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 19:48:19 2008''
+[[Category: Stroppolo ME]]