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4f7i

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==Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH==
==Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH==
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<StructureSection load='4f7i' size='340' side='right' caption='[[4f7i]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='4f7i' size='340' side='right'caption='[[4f7i]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4f7i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F7I FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4f7i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F7I FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPM:3-ISOPROPYLMALIC+ACID'>IPM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
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</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&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2y41|2y41]], [[2y40|2y40]], [[2y3z|2y3z]], [[1hex|1hex]], [[2ztw|2ztw]], [[2y42|2y42]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPM:3-ISOPROPYLMALIC+ACID'>IPM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">leuB, TTHA1230 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4f7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f7i OCA], [https://pdbe.org/4f7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f7i RCSB], [https://www.ebi.ac.uk/pdbsum/4f7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f7i ProSAT]</span></td></tr>
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<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>
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<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=4f7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f7i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4f7i RCSB], [http://www.ebi.ac.uk/pdbsum/4f7i PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/LEU3_THET8 LEU3_THET8] 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.[HAMAP-Rule:MF_01033]
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The three-dimensional structure of the enzyme 3-isopropylmalate dehydrogenase from the bacterium Thermus thermophilus in complex with Mn2+ , its substrate isopropylmalate and its co-factor product NADH at 2.0 A resolution features a fully closed conformation of the enzyme. Upon closure of the two domains, the substrate and the co-factor are brought into precise relative orientation and close proximity, with a distance between the C2 atom of the substrate and the C4N atom of the pyridine ring of the co-factor of approximately 3.0 A. The structure further shows binding of a K+ ion close to the active site, and provides an explanation for its known activating effect. Hence, this structure is an excellent mimic for the enzymatically competent complex. Using high-level QM/MM calculations, it may be demonstrated that, in the observed arrangement of the reactants, transfer of a hydride from the C2 atom of 3-isopropylmalate to the C4N atom of the pyridine ring of NAD+ is easily possible, with an activation energy of approximately 15 kcal.mol-1 . The activation energy increases by approximately 4-6 kcal.mol-1 when the K+ ion is omitted from the calculations. In the most plausible scenario, prior to hydride transfer the epsilon-amino group of Lys185 acts as a general base in the reaction, aiding the deprotonation reaction of 3-isopropylmalate prior to hydride transfer by employing a low-barrier proton shuttle mechanism involving a water molecule. DATABASE: Structural data have been submitted to the Protein Data Bank under accession number 4F7I.
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Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis.,Pallo A, Olah J, Graczer E, Merli A, Zavodszky P, Weiss MS, Vas M FEBS J. 2014 Sep 11. doi: 10.1111/febs.13044. PMID:25211160<ref>PMID:25211160</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==See Also==
==See Also==
*[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]]
*[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: 3-isopropylmalate dehydrogenase]]
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[[Category: Large Structures]]
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[[Category: Thet8]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Graczer, E.]]
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[[Category: Graczer E]]
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[[Category: Pallo, A.]]
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[[Category: Pallo A]]
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[[Category: Vas, M.]]
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[[Category: Vas M]]
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[[Category: Weiss, M S.]]
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[[Category: Weiss MS]]
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[[Category: Zavodszky, P.]]
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[[Category: Zavodszky P]]
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[[Category: 3-ipm-dh]]
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[[Category: Beta-ipm dehydrogenase]]
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[[Category: Imdh]]
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[[Category: Ipmdh]]
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[[Category: Isopropylmalate dehydrogenase]]
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[[Category: Oxidoreductase]]
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Current revision

Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH

PDB ID 4f7i

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