Crystal structure of 4-hydroxyphenylpyruvate dioxygenase in complex with substrate reveals a new starting point for herbicide discovery

Hong Yan Lin, Xi Chen, Jia Nan Chen, Da Wei Wang, Feng Xu Wu, Song Yun Lin, Chang Guo Zhan, Jia Wei Wu, Wen Chao Yang, Guang Fu Yang

Research output: Contribution to journalArticlepeer-review

48 Scopus citations

Abstract

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a promising target for drug and pesticide discovery.Theunknown bindingmode of substrate is still a big challenge for the understanding of enzymatic reaction mechanism and novelHPPD inhibitor design.Herein, we determined the first crystal structure of Arabidopsis thaliana HPPD (AtHPPD) in complex with its natural substrate (HPPA) at a resolution of 2.80 A. 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-AtHPPD and holo-AtHPPD 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 Ki value of 24.10 nM towards AtHPPD. The inhibitor has entered into industry development as the first selective herbicide used for theweed control in sorghum field. The crystal structure of AtHPPD in complex with the inhibitor (2.40 A) 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.

Original languageEnglish
Article number2602414
JournalResearch
Volume2019
DOIs
StatePublished - 2019

Bibliographical note

Funding Information:
We thank Dr. Jiang-Qing Dong for the help in structural analysis and Dr. Jun-Jun Liu for the help in QM-MM calculation. This work was funded in part by the National Key Research and Development Program of China (no. 2017YFD0200500), National Natural Science Foundation of China (nos. 21837001 and 21672079), Hubei Province Natural Science Foundation (no. 2018CFA072), and the self-determined research funds of Central China Normal University (CCNU18ZDPY01 and CCNU18TS007) from the colleges’ basic research and operation of MOE. We thank the Shanghai Synchrotron Radiation Facility for providing the facility support.

Funding Information:
We thankDr. Jiang-QingDong for the help in structural analysis and Dr. Jun-Jun Liu for the help in QM-MMcalculation. This work was funded in part by the National Key Research and Development Programof China (no. 2017YFD0200500), NationalNatural Science Foundation of China (nos. 21837001 and 21672079), Hubei Province Natural Science Foundation (no. 2018CFA072), and the self-determined research funds of Central China Normal University (CCNU18ZDPY01 and CCNU18TS007) from the colleges' basic research and operation of MOE.We thank the Shanghai Synchrotron Radiation Facility for providing the facility support

Publisher Copyright:
Copyright © 2019 Hong-Yan Lin et al.

ASJC Scopus subject areas

  • General

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