3vl3: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
<StructureSection load='3vl3' size='340' side='right'caption='[[3vl3]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='3vl3' size='340' side='right'caption='[[3vl3]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vl3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <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> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</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> | |||
<tr id=' | |||
< | |||
<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> | <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> | </table> | ||
== Function == | == 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;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 28: | Line 26: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Shewanella oneidensis MR-1]] | ||
[[Category: Nagae | [[Category: Nagae T]] | ||
[[Category: Watanabe | [[Category: Watanabe N]] | ||
Latest revision as of 15:24, 8 November 2023
3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 340 MPa3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 340 MPa
Structural highlights
FunctionLEU3_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. Publication Abstract from PubMedHydrostatic 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||