4f7i: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,327,076 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,327,076 edits
No edit summary
 
Line 4: Line 4:
== Structural highlights ==
== Structural highlights ==
<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>
<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>
</td></tr><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>
</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>
<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>
<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>
<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>
</table>
</table>
== Function ==
== Function ==
[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]
[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]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4f7i" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]]
*[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
Retrieved from "https://proteopedia.org/4f7i"