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| | <StructureSection load='6xxy' size='340' side='right'caption='[[6xxy]], [[Resolution|resolution]] 2.09Å' scene=''> | | <StructureSection load='6xxy' size='340' side='right'caption='[[6xxy]], [[Resolution|resolution]] 2.09Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6xxy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XXY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6XXY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6xxy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XXY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XXY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=O45:2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic+acid'>O45</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]] 2.09Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">leuB, HI_0987 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=O45:2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic+acid'>O45</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6xxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xxy OCA], [https://pdbe.org/6xxy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xxy RCSB], [https://www.ebi.ac.uk/pdbsum/6xxy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xxy ProSAT]</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=6xxy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xxy OCA], [http://pdbe.org/6xxy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xxy RCSB], [http://www.ebi.ac.uk/pdbsum/6xxy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xxy ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LEU3_HAEIN LEU3_HAEIN]] 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 (By similarity). | + | [https://www.uniprot.org/uniprot/LEU3_HAEIN LEU3_HAEIN] 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 (By similarity). |
| | <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 6xxy" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6xxy" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Isopropylmalate dehydrogenase|Isopropylmalate dehydrogenase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 3-isopropylmalate dehydrogenase]] | + | [[Category: Haemophilus influenzae Rd KW20]] |
| - | [[Category: Haein]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Martignon, S]] | + | [[Category: Martignon S]] |
| - | [[Category: Miggiano, R]] | + | [[Category: Miggiano R]] |
| - | [[Category: Rizzi, M]] | + | [[Category: Rizzi M]] |
| - | [[Category: Rossi, F]] | + | [[Category: Rossi F]] |
| - | [[Category: Haemophilus influenzae]]
| + | |
| - | [[Category: Inhibitor]]
| + | |
| - | [[Category: Leucine biosyntheti]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
LEU3_HAEIN 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 (By similarity).
Publication Abstract from PubMed
3-isopropylmalate dehydrogenases (LeuB) belong to the leucine biosynthetic pathway and catalyze the irreversible oxidative decarboxylation of 3IPM to 2-ketoisocaproate that is finally converted into leucine by a branched-chain aminotransferase. Since leucine is an essential amino acid for humans, and it is also vital for the growth of many pathogenic bacteria, the enzymes belonging to this pathway can be considered as potential target sites for designing of a new class of antibacterial agents. We have determined the crystal structure of the Haemophilus influenzae LeuB in complex with the cofactor NAD(+) and the inhibitor O-IbOHA, at 2.1 A resolution; moreover, we have investigated the inhibitor mechanism of action by analyzing the enzyme kinetics. The structure of H. influenzae LeuB in complex with the intermediate analog inhibitor displays a fully closed conformation, resembling the previously observed, closed form of the equivalent enzyme of Thiobacillus ferrooxidans in complex with the 3IPM substrate. O-IbOHA was found to bind the active site by adopting the same conformation of 3IPM, and to induce an unreported repositioning of the side chain of the amino acids that participate in the coordination of the ligand. Indeed, the experimentally observed binding mode of O-IbOHA to the H. influenzae LeuB enzyme, reveals aspects of novelty compared to the computational binding prediction performed on M. tuberculosis LeuB. Overall, our data provide new insights for the structure-based rational design of a new class of antibiotics targeting the biosynthesis of leucine in pathogenic bacteria.
Crystal structure of Haemophilus influenzae 3-isopropylmalate dehydrogenase (LeuB) in complex with the inhibitor O-isobutenyl oxalylhydroxamate.,Miggiano R, Martignon S, Minassi A, Rossi F, Rizzi M Biochem Biophys Res Commun. 2020 Feb 11. pii: S0006-291X(20)30288-6. doi:, 10.1016/j.bbrc.2020.02.022. PMID:32059844[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Miggiano R, Martignon S, Minassi A, Rossi F, Rizzi M. Crystal structure of Haemophilus influenzae 3-isopropylmalate dehydrogenase (LeuB) in complex with the inhibitor O-isobutenyl oxalylhydroxamate. Biochem Biophys Res Commun. 2020 Feb 11. pii: S0006-291X(20)30288-6. doi:, 10.1016/j.bbrc.2020.02.022. PMID:32059844 doi:http://dx.doi.org/10.1016/j.bbrc.2020.02.022
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