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| | <StructureSection load='6ovt' size='340' side='right'caption='[[6ovt]], [[Resolution|resolution]] 1.88Å' scene=''> | | <StructureSection load='6ovt' size='340' side='right'caption='[[6ovt]], [[Resolution|resolution]] 1.88Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ovt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OVT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OVT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ovt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OVT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OVT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.88Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ilvD, ilvD_1, DK316_01030, DSI35_17380, ERS027644_00467, ERS027651_01171, ERS027653_01384, ERS027661_02038, ERS124361_01678, SAMEA2682864_00050, SAMEA2683035_00341 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=6ovt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ovt OCA], [https://pdbe.org/6ovt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ovt RCSB], [https://www.ebi.ac.uk/pdbsum/6ovt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ovt 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/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.9 4.2.1.9] </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=6ovt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ovt OCA], [http://pdbe.org/6ovt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ovt RCSB], [http://www.ebi.ac.uk/pdbsum/6ovt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ovt ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ILVD_MYCTU ILVD_MYCTU] Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. Is specific for the (R) isomer of 2,3-dihydroxy-3-methylbutanoate, with no catalytic activity against the (S) isomer.<ref>PMID:31315931</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lyase]] | + | [[Category: Mycobacterium tuberculosis]] |
| - | [[Category: Almo, S C]] | + | [[Category: Almo SC]] |
| - | [[Category: Baker, E N]] | + | [[Category: Baker EN]] |
| - | [[Category: Bashiri, G]] | + | [[Category: Bashiri G]] |
| - | [[Category: Bonanno, J B]] | + | [[Category: Bonanno JB]] |
| - | [[Category: Grove, T L]] | + | [[Category: Grove TL]] |
| - | [[Category: 3-dihydroxy-3-methylbutanoate 3-methyl-2-oxobutanoate]]
| + | |
| - | [[Category: Dihydroxy-acid dehydratase 2]]
| + | |
| Structural highlights
6ovt is a 4 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.88Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
ILVD_MYCTU Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively. Is specific for the (R) isomer of 2,3-dihydroxy-3-methylbutanoate, with no catalytic activity against the (S) isomer.[1]
Publication Abstract from PubMed
Iron-sulfur clusters are protein cofactors with an ancient evolutionary origin. These clusters are best known for their roles in redox proteins such as ferredoxins, but some iron-sulfur clusters have nonredox roles in the active sites of enzymes. Such clusters are often prone to oxidative degradation, making the enzymes difficult to characterize. Here we report a structural and functional characterization of dihydroxyacid dehydratase (DHAD) from Mycobacterium tuberculosis (Mtb), an essential enzyme in the biosynthesis of branched-chain amino acids. Conducting this analysis under fully anaerobic conditions, we solved the DHAD crystal structure, at 1.88 A resolution, revealing a 2Fe-2S cluster in which one iron ligand is a potentially exchangeable water molecule or hydroxide. UV and EPR spectroscopy both suggested that the substrate binds directly to the cluster or very close to it. Kinetic analysis implicated two ionizable groups in the catalytic mechanism, which we postulate to be Ser-491 and the iron-bound water/hydroxide. Site-directed mutagenesis showed that Ser-491 is essential for activity, and substrate docking indicated that this residue is perfectly placed for proton abstraction. We found that a bound Mg(2+) ion 6.5 A from the 2Fe-2S cluster plays a key role in substrate binding. We also identified a putative entry channel that enables access to the cluster and show that Mtb-DHAD is inhibited by a recently discovered herbicide, aspterric acid, that, given the essentiality of DHAD for Mtb survival, is a potential lead compound for the design of novel anti-TB drugs.
The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster.,Bashiri G, Grove TL, Hegde SS, Lagautriere T, Gerfen GJ, Almo SC, Squire CJ, Blanchard JS, Baker EN J Biol Chem. 2019 Aug 30;294(35):13158-13170. doi: 10.1074/jbc.RA119.009498. Epub, 2019 Jul 16. PMID:31315931[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bashiri G, Grove TL, Hegde SS, Lagautriere T, Gerfen GJ, Almo SC, Squire CJ, Blanchard JS, Baker EN. The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster. J Biol Chem. 2019 Aug 30;294(35):13158-13170. doi: 10.1074/jbc.RA119.009498. Epub, 2019 Jul 16. PMID:31315931 doi:http://dx.doi.org/10.1074/jbc.RA119.009498
- ↑ Bashiri G, Grove TL, Hegde SS, Lagautriere T, Gerfen GJ, Almo SC, Squire CJ, Blanchard JS, Baker EN. The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster. J Biol Chem. 2019 Aug 30;294(35):13158-13170. doi: 10.1074/jbc.RA119.009498. Epub, 2019 Jul 16. PMID:31315931 doi:http://dx.doi.org/10.1074/jbc.RA119.009498
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