The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster
© 2019 Bashiri et al..
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 Å 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 Mg2+ ion 6.5 Å 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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2019 |
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| Erschienen: |
2019 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:294 |
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| Enthalten in: |
The Journal of biological chemistry - 294(2019), 35 vom: 30. Aug., Seite 13158-13170 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Bashiri, Ghader [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 30.03.2020 Date Revised 17.03.2021 published: Print-Electronic PDB: 6ovt Citation Status MEDLINE |
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| doi: |
10.1074/jbc.RA119.009498 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM299284875 |
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| 041 | |a eng | ||
| 100 | 1 | |a Bashiri, Ghader |e verfasserin |4 aut | |
| 245 | 1 | 4 | |a The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster |
| 264 | 1 | |c 2019 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 30.03.2020 | ||
| 500 | |a Date Revised 17.03.2021 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a PDB: 6ovt | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2019 Bashiri et al. | ||
| 520 | |a 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 Å 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 Mg2+ ion 6.5 Å 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 | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, N.I.H., Extramural | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Mycobacterium tuberculosis | |
| 650 | 4 | |a biosynthesis | |
| 650 | 4 | |a crystal structure | |
| 650 | 4 | |a dihydroxyacid dehydratase | |
| 650 | 4 | |a iron–sulfur protein | |
| 650 | 4 | |a protein stability | |
| 650 | 4 | |a protein structure | |
| 650 | 7 | |a Amino Acids, Branched-Chain |2 NLM | |
| 650 | 7 | |a Iron-Sulfur Proteins |2 NLM | |
| 650 | 7 | |a Hydro-Lyases |2 NLM | |
| 650 | 7 | |a EC 4.2.1.- |2 NLM | |
| 650 | 7 | |a dihydroxyacid dehydratase |2 NLM | |
| 650 | 7 | |a EC 4.2.1.9 |2 NLM | |
| 700 | 1 | |a Grove, Tyler L |e verfasserin |4 aut | |
| 700 | 1 | |a Hegde, Subray S |e verfasserin |4 aut | |
| 700 | 1 | |a Lagautriere, Thomas |e verfasserin |4 aut | |
| 700 | 1 | |a Gerfen, Gary J |e verfasserin |4 aut | |
| 700 | 1 | |a Almo, Steven C |e verfasserin |4 aut | |
| 700 | 1 | |a Squire, Christopher J |e verfasserin |4 aut | |
| 700 | 1 | |a Blanchard, John S |e verfasserin |4 aut | |
| 700 | 1 | |a Baker, Edward N |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t The Journal of biological chemistry |d 1945 |g 294(2019), 35 vom: 30. Aug., Seite 13158-13170 |w (DE-627)NLM000004995 |x 1083-351X |7 nnns |
| 773 | 1 | 8 | |g volume:294 |g year:2019 |g number:35 |g day:30 |g month:08 |g pages:13158-13170 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1074/jbc.RA119.009498 |3 Volltext |
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