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Molecular basis for the inhibition of β-hydroxyacyl-ACP dehydratase HadAB complex from Mycobacterium tuberculosis by flavonoid inhibitors.

Dong Y, Qiu X, Shaw N, Xu Y, Sun Y, Li X, Li J, Rao Z - Protein Cell (2015)

Bottom Line: We show that inhibitors bind in this cavity and protrude into the substrate binding channel.Thus, inhibitors of MtbHadAB exert their effect by occluding substrate from the active site.The unveiling of this mechanism of inhibition paves the way for accelerating development of next generation of anti-TB drugs.

View Article: PubMed Central - PubMed

Affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

ABSTRACT
Dehydration is one of the key steps in the biosynthesis of mycolic acids and is vital to the growth of Mycobacterium tuberculosis (Mtb). Consequently, stalling dehydration cures tuberculosis (TB). Clinically used anti-TB drugs like thiacetazone (TAC) and isoxyl (ISO) as well as flavonoids inhibit the enzyme activity of the β-hydroxyacyl-ACP dehydratase HadAB complex. How this inhibition is exerted, has remained an enigma for years. Here, we describe the first crystal structures of the MtbHadAB complex bound with flavonoid inhibitor butein, 2',4,4'-trihydroxychalcone or fisetin. Despite sharing no sequence identity from Blast, HadA and HadB adopt a very similar hotdog fold. HadA forms a tight dimer with HadB in which the proteins are sitting side-by-side, but are oriented anti-parallel. While HadB contributes the catalytically critical His-Asp dyad, HadA binds the fatty acid substrate in a long channel. The atypical double hotdog fold with a single active site formed by MtbHadAB gives rise to a long, narrow cavity that vertically traverses the fatty acid binding channel. At the base of this cavity lies Cys61, which upon mutation to Ser confers drug-resistance in TB patients. We show that inhibitors bind in this cavity and protrude into the substrate binding channel. Thus, inhibitors of MtbHadAB exert their effect by occluding substrate from the active site. The unveiling of this mechanism of inhibition paves the way for accelerating development of next generation of anti-TB drugs.

No MeSH data available.


Related in: MedlinePlus

Sequence alignment of HadA and HadB with secondary structural elements marked near the sequence. HadA does not share any significant primary sequence identity with HadB from Blast (or only 13.57% identity calculated by ClustalW2), but their secondary structural elements distribution is similar
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Fig2: Sequence alignment of HadA and HadB with secondary structural elements marked near the sequence. HadA does not share any significant primary sequence identity with HadB from Blast (or only 13.57% identity calculated by ClustalW2), but their secondary structural elements distribution is similar

Mentions: HadA does not share any significant primary sequence identity with HadB from Blast (Fig. 2, showed by ESPript server (Robert and Gouet, 2014)). In spite of this, the overall structure of the MtbHadAB complex reveals that both proteins adopt a similar hotdog fold (Fig. 3B). A central sheet composed of five strands (β1–β5) is twisted to form a concave cavity at the center. A hotdog helix, α3, (referred to as αHD hereafter) is embedded laterally in this cavity, giving the appearance of a typical hotdog fold. Helices α1 and α2 are inserted between strand β1 and αHD. Two such folds, one each contributed by HadA and HadB, sitting side-by-side, but oriented anti-parallel, result in a double hotdog fold. Thus, the overall structure of MtbHadAB complex consists of a double hotdog fold (Fig. 3A).Figure 3


Molecular basis for the inhibition of β-hydroxyacyl-ACP dehydratase HadAB complex from Mycobacterium tuberculosis by flavonoid inhibitors.

Dong Y, Qiu X, Shaw N, Xu Y, Sun Y, Li X, Li J, Rao Z - Protein Cell (2015)

Sequence alignment of HadA and HadB with secondary structural elements marked near the sequence. HadA does not share any significant primary sequence identity with HadB from Blast (or only 13.57% identity calculated by ClustalW2), but their secondary structural elements distribution is similar
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4491049&req=5

Fig2: Sequence alignment of HadA and HadB with secondary structural elements marked near the sequence. HadA does not share any significant primary sequence identity with HadB from Blast (or only 13.57% identity calculated by ClustalW2), but their secondary structural elements distribution is similar
Mentions: HadA does not share any significant primary sequence identity with HadB from Blast (Fig. 2, showed by ESPript server (Robert and Gouet, 2014)). In spite of this, the overall structure of the MtbHadAB complex reveals that both proteins adopt a similar hotdog fold (Fig. 3B). A central sheet composed of five strands (β1–β5) is twisted to form a concave cavity at the center. A hotdog helix, α3, (referred to as αHD hereafter) is embedded laterally in this cavity, giving the appearance of a typical hotdog fold. Helices α1 and α2 are inserted between strand β1 and αHD. Two such folds, one each contributed by HadA and HadB, sitting side-by-side, but oriented anti-parallel, result in a double hotdog fold. Thus, the overall structure of MtbHadAB complex consists of a double hotdog fold (Fig. 3A).Figure 3

Bottom Line: We show that inhibitors bind in this cavity and protrude into the substrate binding channel.Thus, inhibitors of MtbHadAB exert their effect by occluding substrate from the active site.The unveiling of this mechanism of inhibition paves the way for accelerating development of next generation of anti-TB drugs.

View Article: PubMed Central - PubMed

Affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

ABSTRACT
Dehydration is one of the key steps in the biosynthesis of mycolic acids and is vital to the growth of Mycobacterium tuberculosis (Mtb). Consequently, stalling dehydration cures tuberculosis (TB). Clinically used anti-TB drugs like thiacetazone (TAC) and isoxyl (ISO) as well as flavonoids inhibit the enzyme activity of the β-hydroxyacyl-ACP dehydratase HadAB complex. How this inhibition is exerted, has remained an enigma for years. Here, we describe the first crystal structures of the MtbHadAB complex bound with flavonoid inhibitor butein, 2',4,4'-trihydroxychalcone or fisetin. Despite sharing no sequence identity from Blast, HadA and HadB adopt a very similar hotdog fold. HadA forms a tight dimer with HadB in which the proteins are sitting side-by-side, but are oriented anti-parallel. While HadB contributes the catalytically critical His-Asp dyad, HadA binds the fatty acid substrate in a long channel. The atypical double hotdog fold with a single active site formed by MtbHadAB gives rise to a long, narrow cavity that vertically traverses the fatty acid binding channel. At the base of this cavity lies Cys61, which upon mutation to Ser confers drug-resistance in TB patients. We show that inhibitors bind in this cavity and protrude into the substrate binding channel. Thus, inhibitors of MtbHadAB exert their effect by occluding substrate from the active site. The unveiling of this mechanism of inhibition paves the way for accelerating development of next generation of anti-TB drugs.

No MeSH data available.


Related in: MedlinePlus