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| | ==3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 580 MPa== | | ==3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 580 MPa== |
| - | <StructureSection load='3vl6' size='340' side='right' caption='[[3vl6]], [[Resolution|resolution]] 2.07Å' scene=''> | + | <StructureSection load='3vl6' size='340' side='right'caption='[[3vl6]], [[Resolution|resolution]] 2.07Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3vl6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VL6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VL6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3vl6]] 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=3VL6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VL6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.07Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vlz|3vlz]], [[3vl2|3vl2]], [[3vl3|3vl3]], [[3vl4|3vl4]], [[3vl7|3vl7]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">leuB, SO_4235 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</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=3vl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vl6 OCA], [https://pdbe.org/3vl6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vl6 RCSB], [https://www.ebi.ac.uk/pdbsum/3vl6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vl6 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-isopropylmalate_dehydrogenase 3-isopropylmalate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.85 1.1.1.85] </span></td></tr> | + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vl6 OCA], [http://pdbe.org/3vl6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vl6 RCSB], [http://www.ebi.ac.uk/pdbsum/3vl6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vl6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. | + | [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 == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 3vl6" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 3vl6" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 3-isopropylmalate dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Sheon]] | + | [[Category: Shewanella oneidensis MR-1]] |
| - | [[Category: Nagae, T]] | + | [[Category: Nagae T]] |
| - | [[Category: Watanabe, N]] | + | [[Category: Watanabe N]] |
| - | [[Category: Dac]]
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| - | [[Category: Diamond-anvil cell]]
| + | |
| - | [[Category: High-pressure]]
| + | |
| - | [[Category: Ipmdh]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
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.
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.
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 Also
References
- ↑ Nagae T, Kawamura T, Chavas LM, Niwa K, Hasegawa M, Kato C, Watanabe N. High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase. Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):300-9. Epub 2012 Feb 14. PMID:22349232 doi:http://dx.doi.org/10.1107/S0907444912001862
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