5XGK

Crystal structure of Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase (AtHPPD) complexed with its substrate 4-hydroxyphenylpyruvate acid (HPPA)

Summary for 5XGK

• Entry DOI: 10.2210/pdb5xgk/pdb
• Related: 1SP9
• Descriptor: 4-hydroxyphenylpyruvate dioxygenase, (2S)-2-hydroxy-3-(4-hydroxyphenyl)propanoic acid, FE (III) ION, ... (5 entities in total)
• Functional Keywords: 4-hydroxyphenylpyruvate dioxygenase, catalytic mechanism, drug discovery, oxidoreductase
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 4
• Total formula weight: 196137.06

Authors

Yang, G.F.,Yang, W.C.,Lin, H.Y. (deposition date: 2017-04-14, release date: 2018-09-19, Last modification date: 2023-11-22)

Primary citation

Lin, H.Y.,Chen, X.,Chen, J.N.,Wang, D.W.,Wu, F.X.,Lin, S.Y.,Zhan, C.G.,Wu, J.W.,Yang, W.C.,Yang, G.F.
Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery.
Res, 2019:2602414-2602414, 2019

PubMed Abstract: 4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a promising target for drug and pesticide discovery. The unknown binding mode of substrate is still a big challenge for the understanding of enzymatic reaction mechanism and novel HPPD inhibitor design. Herein, we determined the first crystal structure of HPPD (HPPD) in complex with its natural substrate (HPPA) at a resolution of 2.80 Å. Then, combination of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations confirmed that HPPA takes keto rather than enol form inside the HPPD active pocket. Subsequent site-directed mutagenesis and kinetic analysis further showed that residues (Phe424, Asn423, Glu394, Gln307, Asn282, and Ser267) played important roles in substrate binding and catalytic cycle. Structural comparison between HPPA-HPPD and holo-HPPD revealed that Gln293 underwent a remarkable rotation upon the HPPA binding and formed H-bond network of Ser267-Asn282-Gln307-Gln293, resulting in the transformation of HPPD from an inactive state to active state. Finally, taking the conformation change of Gln293 as a target, we proposed a new strategy of blocking the transformation of HPPD from inactive state to active state to design a novel inhibitor with value of 24.10 nM towards HPPD. The inhibitor has entered into industry development as the first selective herbicide used for the weed control in sorghum field. The crystal structure of HPPD in complex with the inhibitor (2.40 Å) confirmed the rationality of the design strategy. We believe that the present work provides a new starting point for the understanding of enzymatic reaction mechanism and the design of next generation HPPD inhibitors.

PubMed: 31549053
DOI: 10.34133/2019/2602414

Experimental method

X-RAY DIFFRACTION (2.8 Å)