1v04: Difference between revisions

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

OCA

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-[[Image:1v04.png|left|200px]]
-<!--
+==serum paraoxonase by directed evolution==
-The line below this paragraph, containing "STRUCTURE_1v04", creates the "Structure Box" on the page.
+<StructureSection load='1v04' size='340' side='right'caption='[[1v04]], [[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'>[[1v04]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens], [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus], [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] and [https://en.wikipedia.org/wiki/Rattus_rattus Rattus rattus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V04 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_1v04|  PDB=1v04  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v04 OCA], [https://pdbe.org/1v04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v04 RCSB], [https://www.ebi.ac.uk/pdbsum/1v04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v04 ProSAT], [https://www.topsan.org/Proteins/ISPC/1v04 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PON1_RABIT PON1_RABIT] Hydrolyzes the toxic metabolites of a variety of organophosphorus insecticides. Capable of hydrolyzing a broad spectrum of organophosphate substrates and lactones, and a number of aromatic carboxylic acid esters. Mediates an enzymatic protection of low density lipoproteins against oxidative modification.<ref>PMID:11266077</ref>
+== 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/v0/1v04_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=1v04 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Members of the serum paraoxonase (PON) family have been identified in mammals and other vertebrates, and in invertebrates. PONs exhibit a wide range of physiologically important hydrolytic activities, including drug metabolism and detoxification of nerve agents. PON1 and PON3 reside on high-density lipoprotein (HDL, 'good cholesterol') and are involved in the prevention of atherosclerosis. We describe the first crystal structure of a PON family member, a variant of PON1 obtained by directed evolution, at a resolution of 2.2 A. PON1 is a six-bladed beta-propeller with a unique active site lid that is also involved in HDL binding. The three-dimensional structure and directed evolution studies permit a detailed description of PON1's active site and catalytic mechanism, which are reminiscent of secreted phospholipase A2, and of the routes by which PON family members diverged toward different substrate and reaction selectivities.
-===SERUM PARAOXONASE BY DIRECTED EVOLUTION===
+Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes.,Harel M, Aharoni A, Gaidukov L, Brumshtein B, Khersonsky O, Meged R, Dvir H, Ravelli RB, McCarthy A, Toker L, Silman I, Sussman JL, Tawfik DS Nat Struct Mol Biol. 2004 May;11(5):412-9. Epub 2004 Apr 18. PMID:15098021<ref>PMID:15098021</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_15098021}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1v04" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15098021 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_15098021}}
-==About this Structure==
-[[1v04]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens,_oryctolagus_cuniculus,_mus_musculus,_rattus_rattus Homo sapiens, oryctolagus cuniculus, mus musculus, rattus rattus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V04 OCA].
 ==See Also==
-*[[Favorites]]
+*[[Serum Paraoxonase|Serum Paraoxonase]]
-*[[Joel Sussman's Favorites]]
+== References ==
-*[[User:Boris Brumshtein]]
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-<ref group="xtra">PMID:015098021</ref><references group="xtra"/>
+[[Category: Homo sapiens]]
-[[Category: Homo sapiens, oryctolagus cuniculus, mus musculus, rattus rattus]]
+[[Category: Large Structures]]
-[[Category: Aharoni, A.]]
+[[Category: Mus musculus]]
-[[Category: Brumshtein, B.]]
+[[Category: Oryctolagus cuniculus]]
-[[Category: Dvir, H.]]
+[[Category: Rattus rattus]]
-[[Category: Gaidukov, L.]]
+[[Category: Aharoni A]]
-[[Category: Harel, M.]]
+[[Category: Brumshtein B]]
-[[Category: Khersonsky, O.]]
+[[Category: Dvir H]]
-[[Category: Mccarthy, A.]]
+[[Category: Gaidukov L]]
-[[Category: Meged, R.]]
+[[Category: Harel M]]
-[[Category: Ravelli, R B.G.]]
+[[Category: Khersonsky O]]
-[[Category: Silman, I.]]
+[[Category: McCarthy A]]
-[[Category: Sussman, J L.]]
+[[Category: Meged R]]
-[[Category: Tawfik, D S.]]
+[[Category: Ravelli RBG]]
-[[Category: Toker, L.]]
+[[Category: Silman I]]
-[[Category: Yagur, S.]]
+[[Category: Sussman JL]]
-[[Category: Antioxidant]]
+[[Category: Tawfik DS]]
-[[Category: Directed evolution]]
+[[Category: Toker L]]
-[[Category: Hydrolase]]
+[[Category: Yagur S]]
-[[Category: ISPC]]
-[[Category: Israel Structural Proteomics Center]]
-[[Category: Paraoxonase]]
-[[Category: Structural genomic]]