1ibf: Difference between revisions

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-[[Image:1ibf.png|left|200px]]
-<!--
+==X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G==
-The line below this paragraph, containing "STRUCTURE_1ibf", creates the "Structure Box" on the page.
+<StructureSection load='1ibf' size='340' side='right'caption='[[1ibf]], [[Resolution|resolution]] 2.20&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'>[[1ibf]] 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=1IBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IBF 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]] 2.2&#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>
-{{STRUCTURE_1ibf|  PDB=1ibf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [https://pdbe.org/1ibf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [https://www.ebi.ac.uk/pdbsum/1ibf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibf 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/1ibf_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=1ibf 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.
-===X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_11327787}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ibf" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11327787 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_11327787}}
-==About this Structure==
-[[1ibf]] is a 1 chain structure of [[Superoxide Dismutase]] with 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=1IBF OCA].
 ==See Also==
-*[[Superoxide Dismutase]]
+*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:11327787</ref><references group="xtra"/>
+__TOC__
-[[Category: Photobacterium leiognathi]]
+</StructureSection>
-[[Category: Superoxide dismutase]]
+[[Category: Large Structures]]
-[[Category: Battistoni, A.]]
+[[Category: Photobacterium leiognathi subsp. leiognathi]]
-[[Category: Bolognesi, M.]]
+[[Category: Battistoni A]]
-[[Category: Bordo, D.]]
+[[Category: Bolognesi M]]
-[[Category: Desideri, A.]]
+[[Category: Bordo D]]
-[[Category: Milani, M.]]
+[[Category: D'Orazio M]]
-[[Category: Neill, P O.]]
+[[Category: Desideri A]]
-[[Category: Orazio, M D.]]
+[[Category: Milani M]]
-[[Category: Pesce, A.]]
+[[Category: O'Neill P]]
-[[Category: Rosano, C.]]
+[[Category: Pesce A]]
-[[Category: Stroppolo, M E.]]
+[[Category: Rosano C]]
-[[Category: Oxidoreductase]]
+[[Category: Stroppolo ME]]
-[[Category: Prokaryotic superoxide dismutase]]
-[[Category: Subunit interaction]]