1bzo: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1bzo.png|left|200px]]
-<!--
+==THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.==
-The line below this paragraph, containing "STRUCTURE_1bzo", creates the "Structure Box" on the page.
+<StructureSection load='1bzo' size='340' side='right'caption='[[1bzo]], [[Resolution|resolution]] 2.10&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'>[[1bzo]] 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=1BZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BZO 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]] 2.1&#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=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1bzo|  PDB=1bzo  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [https://pdbe.org/1bzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [https://www.ebi.ac.uk/pdbsum/1bzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bzo 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/bz/1bzo_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=1bzo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Prokaryotic Cu,Zn superoxide dismutases are characterized by a distinct quaternary structure, as compared to that of the homologous eukaryotic enzymes. Here we report a newly determined crystal structure of the dimeric Cu,Zn superoxide dismutase from Photobacterium leiognathi (crystallized in space group R32, refined at 2.5 A resolution, R-factor 0.19) and analyse it in comparison with that of the monomeric enzyme from Escherichia coli. The dimeric assembly, observed also in a previously studied monoclinic crystal form of P. leiognathi Cu,Zn superoxide dismutase, is based on a ring-shaped subunit contact region, defining a solvated interface cavity. Three clusters of neighbouring residues play a direct role in the stabilization of the quaternary assembly. The present analysis, extended to the amino acid sequences of the other 11 known prokaryotic Cu,Zn superoxide dismutases, shows that at least in five other prokaryotic enzymes the interface residue clusters are under strong evolutionary constraint, suggesting the attainment of a quaternary structure coincident with that of P. leiognathi Cu,Zn superoxide dismutase. Calculation of electrostatic fields for both the enzymes from E. coli and P. leiognathi shows that the monomeric/dimeric association behaviour displayed by prokaryotic Cu, Zn superoxide dismutases is related to the distribution of surface charged residues. Moreover, Brownian dynamics simulations reproduce closely the observed enzyme:substrate association rates, highlighting the role of the active site neighbouring residues in determining the dismutase catalytic properties.
-===THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.===
+Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.,Bordo D, Matak D, Djinovic-Carugo K, Rosano C, Pesce A, Bolognesi M, Stroppolo ME, Falconi M, Battistoni A, Desideri A J Mol Biol. 1999 Jan 8;285(1):283-96. PMID:9878406<ref>PMID:9878406</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1bzo" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9878406}}, adds the Publication Abstract to the page
+*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9878406 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9878406}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-BZO 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=1BZO OCA].
+[[Category: Photobacterium leiognathi subsp. leiognathi]]
+[[Category: Battistoni A]]
-==Reference==
+[[Category: Bolognesi M]]
-Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase., Bordo D, Matak D, Djinovic-Carugo K, Rosano C, Pesce A, Bolognesi M, Stroppolo ME, Falconi M, Battistoni A, Desideri A, J Mol Biol. 1999 Jan 8;285(1):283-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9878406 9878406]
+[[Category: Bordo D]]
-[[Category: Photobacterium leiognathi]]
+[[Category: Desideri A]]
-[[Category: Single protein]]
+[[Category: Djinovic-Carugo K]]
-[[Category: Superoxide dismutase]]
+[[Category: Falconi M]]
-[[Category: Battistoni, A.]]
+[[Category: Matak D]]
-[[Category: Bolognesi, M.]]
+[[Category: Pesce A]]
-[[Category: Bordo, D.]]
+[[Category: Rosano C]]
-[[Category: Desideri, A.]]
+[[Category: Stroppolo ME]]
-[[Category: Djinovic-Carugo, K.]]
-[[Category: Falconi, M.]]
-[[Category: Matak, D.]]
-[[Category: Pesce, A.]]
-[[Category: Rosano, C.]]
-[[Category: Stroppolo, M E.]]
-[[Category: Monomeric cu]]
-[[Category: Protein electrostatic]]
-[[Category: Protein-subunit recognition]]
-[[Category: Zn superoxide dismutase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 20:00:18 2008''