Limits...
ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase.

Zhou H, Sun L, Yang XL, Schimmel P - Nature (2012)

Bottom Line: Thus, HF is a new type of ATP-dependent inhibitor that simultaneously occupies two different substrate binding sites on ProRS.Moreover, our structure indicates a possible similar mechanism of action for febrifugine in malaria treatment.Finally, the elucidation here of a two-site modular targeting activity of HF raises the possibility that substrate-directed capture of similar inhibitors might be a general mechanism that could be applied to other synthetases.

View Article: PubMed Central - PubMed

Affiliation: The Skaggs Institute for Chemical Biology, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

ABSTRACT
Febrifugine is the active component of the Chinese herb Chang Shan (Dichroa febrifuga Lour.), which has been used for treating malaria-induced fever for about 2,000 years. Halofuginone (HF), the halogenated derivative of febrifugine, has been tested in clinical trials for potential therapeutic applications in cancer and fibrotic disease. Recently, HF was reported to inhibit T(H)17 cell differentiation by activating the amino acid response pathway, through inhibiting human prolyl-transfer RNA synthetase (ProRS) to cause intracellular accumulation of uncharged tRNA. Curiously, inhibition requires the presence of unhydrolysed ATP. Here we report an unusual 2.0 Å structure showing that ATP directly locks onto and orients two parts of HF onto human ProRS, so that one part of HF mimics bound proline and the other mimics the 3' end of bound tRNA. Thus, HF is a new type of ATP-dependent inhibitor that simultaneously occupies two different substrate binding sites on ProRS. Moreover, our structure indicates a possible similar mechanism of action for febrifugine in malaria treatment. Finally, the elucidation here of a two-site modular targeting activity of HF raises the possibility that substrate-directed capture of similar inhibitors might be a general mechanism that could be applied to other synthetases.

Show MeSH

Related in: MedlinePlus

Structure of human ProRS and of bound ligandsa, Chemical structures of halofuginone (HF) and the ATP analog (ATPa). b, Two ProRS monomers form an asymmetric unit that is a homodimer. HF and ATPa are shown as spherical models at the active site of both subunits. Here and throughout, ATPa and HF are colored as in Fig.1a. c, HF is buried at the bottom of the pocket and covered by co-bound ATPa. A simulated annealing omit map was calculated with Fourier coefficients 2Fo-Fc, and contoured at 1.5σ.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3569068&req=5

Figure 1: Structure of human ProRS and of bound ligandsa, Chemical structures of halofuginone (HF) and the ATP analog (ATPa). b, Two ProRS monomers form an asymmetric unit that is a homodimer. HF and ATPa are shown as spherical models at the active site of both subunits. Here and throughout, ATPa and HF are colored as in Fig.1a. c, HF is buried at the bottom of the pocket and covered by co-bound ATPa. A simulated annealing omit map was calculated with Fourier coefficients 2Fo-Fc, and contoured at 1.5σ.

Mentions: In its simplest description, HF is comprised of a hydroxypiperidine ring joined by bridging atoms to a double ring halogenated 4-quinazolinone (Fig. 1a). To clarify the mechanism of inhibition of HF, we cloned and expressed human ProRS and were able to obtain co-crystals with a non-hydrolyzable ATP analog ((adenosine 5′-(β,γ-imido)triphosphate)(ATPa)) and HF, which diffracted to 2.0 Å resolution (Supplementary Table 1). The structure was solved by molecular replacement using T. thermophilus ProRS as template. The asymmetric unit contained two ProRS molecules that formed a homodimer (Fig. 1b), as also seen in gel filtration experiments. Each subunit encoded an N-terminal catalytic domain characteristic of a class II tRNA synthetase, an anticodon-binding domain, and a C-terminal zinc-binding domain (Fig. 1b). In the two catalytic domains of the ProRS homodimer, HF and ATPa were bound to the active site for Pro-AMP formation (Fig. 1b, c).


ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase.

Zhou H, Sun L, Yang XL, Schimmel P - Nature (2012)

Structure of human ProRS and of bound ligandsa, Chemical structures of halofuginone (HF) and the ATP analog (ATPa). b, Two ProRS monomers form an asymmetric unit that is a homodimer. HF and ATPa are shown as spherical models at the active site of both subunits. Here and throughout, ATPa and HF are colored as in Fig.1a. c, HF is buried at the bottom of the pocket and covered by co-bound ATPa. A simulated annealing omit map was calculated with Fourier coefficients 2Fo-Fc, and contoured at 1.5σ.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3569068&req=5

Figure 1: Structure of human ProRS and of bound ligandsa, Chemical structures of halofuginone (HF) and the ATP analog (ATPa). b, Two ProRS monomers form an asymmetric unit that is a homodimer. HF and ATPa are shown as spherical models at the active site of both subunits. Here and throughout, ATPa and HF are colored as in Fig.1a. c, HF is buried at the bottom of the pocket and covered by co-bound ATPa. A simulated annealing omit map was calculated with Fourier coefficients 2Fo-Fc, and contoured at 1.5σ.
Mentions: In its simplest description, HF is comprised of a hydroxypiperidine ring joined by bridging atoms to a double ring halogenated 4-quinazolinone (Fig. 1a). To clarify the mechanism of inhibition of HF, we cloned and expressed human ProRS and were able to obtain co-crystals with a non-hydrolyzable ATP analog ((adenosine 5′-(β,γ-imido)triphosphate)(ATPa)) and HF, which diffracted to 2.0 Å resolution (Supplementary Table 1). The structure was solved by molecular replacement using T. thermophilus ProRS as template. The asymmetric unit contained two ProRS molecules that formed a homodimer (Fig. 1b), as also seen in gel filtration experiments. Each subunit encoded an N-terminal catalytic domain characteristic of a class II tRNA synthetase, an anticodon-binding domain, and a C-terminal zinc-binding domain (Fig. 1b). In the two catalytic domains of the ProRS homodimer, HF and ATPa were bound to the active site for Pro-AMP formation (Fig. 1b, c).

Bottom Line: Thus, HF is a new type of ATP-dependent inhibitor that simultaneously occupies two different substrate binding sites on ProRS.Moreover, our structure indicates a possible similar mechanism of action for febrifugine in malaria treatment.Finally, the elucidation here of a two-site modular targeting activity of HF raises the possibility that substrate-directed capture of similar inhibitors might be a general mechanism that could be applied to other synthetases.

View Article: PubMed Central - PubMed

Affiliation: The Skaggs Institute for Chemical Biology, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

ABSTRACT
Febrifugine is the active component of the Chinese herb Chang Shan (Dichroa febrifuga Lour.), which has been used for treating malaria-induced fever for about 2,000 years. Halofuginone (HF), the halogenated derivative of febrifugine, has been tested in clinical trials for potential therapeutic applications in cancer and fibrotic disease. Recently, HF was reported to inhibit T(H)17 cell differentiation by activating the amino acid response pathway, through inhibiting human prolyl-transfer RNA synthetase (ProRS) to cause intracellular accumulation of uncharged tRNA. Curiously, inhibition requires the presence of unhydrolysed ATP. Here we report an unusual 2.0 Å structure showing that ATP directly locks onto and orients two parts of HF onto human ProRS, so that one part of HF mimics bound proline and the other mimics the 3' end of bound tRNA. Thus, HF is a new type of ATP-dependent inhibitor that simultaneously occupies two different substrate binding sites on ProRS. Moreover, our structure indicates a possible similar mechanism of action for febrifugine in malaria treatment. Finally, the elucidation here of a two-site modular targeting activity of HF raises the possibility that substrate-directed capture of similar inhibitors might be a general mechanism that could be applied to other synthetases.

Show MeSH
Related in: MedlinePlus