3vl3: Difference between revisions

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-[[Image:3vl3.jpg|left|200px]]
-<!--
+==3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 340 MPa==
-The line below this paragraph, containing "STRUCTURE_3vl3", creates the "Structure Box" on the page.
+<StructureSection load='3vl3' size='340' side='right'caption='[[3vl3]], [[Resolution|resolution]] 1.80&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'>[[3vl3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VL3 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]] 1.8&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPM:3-ISOPROPYLMALIC+ACID'>IPM</scene></td></tr>
-{{STRUCTURE_3vl3|  PDB=3vl3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vl3 OCA], [https://pdbe.org/3vl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vl3 RCSB], [https://www.ebi.ac.uk/pdbsum/3vl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vl3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LEU3_SHEON LEU3_SHEON] Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hydrostatic pressure induces structural changes in proteins, including denaturation, the mechanism of which has been attributed to water penetration into the protein interior. In this study, structures of 3-isopropylmalate dehydrogenase (IPMDH) from Shewanella oneidensis MR-1 were determined at about 2 A resolution under pressures ranging from 0.1 to 650 MPa using a diamond anvil cell (DAC). Although most of the protein cavities are monotonically compressed as the pressure increases, the volume of one particular cavity at the dimer interface increases at pressures over 340 MPa. In parallel with this volume increase, water penetration into the cavity could be observed at pressures over 410 MPa. In addition, the generation of a new cleft on the molecular surface accompanied by water penetration could also be observed at pressures over 580 MPa. These water-penetration phenomena are considered to be initial steps in the pressure-denaturation process of IPMDH.
-===3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 340 MPa===
+High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase.,Nagae T, Kawamura T, Chavas LM, Niwa K, Hasegawa M, Kato C, Watanabe N Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):300-9. Epub 2012 Feb 14. PMID:22349232<ref>PMID:22349232</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3vl3" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[3vl3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VL3 OCA].
+*[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]]
-[[Category: 3-isopropylmalate dehydrogenase]]
+== References ==
-[[Category: Shewanella oneidensis]]
+<references/>
-[[Category: Nagae, T.]]
+__TOC__
-[[Category: Watanabe, N.]]
+</StructureSection>
-[[Category: Decarboxylating dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: High pressure]]
+[[Category: Shewanella oneidensis MR-1]]
-[[Category: Oxidoreductase]]
+[[Category: Nagae T]]
+[[Category: Watanabe N]]