Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism

Wen Chi Cheng, Yen Fu Chen, Hung Jung Wang, Kai Cheng Hsu, Shuang Chih Lin, Tzu Jung Chen, Jinn Moon Yang, Wen Ching Wang

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

Shikimate kinase (SK), which catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP, is the enzyme in the fifth step of the shikimate pathway for biosynthesis of aromatic amino acids. This pathway is present in bacteria, fungi, and plants but absent in mammals and therefore represents an attractive target pathway for the development of new antimicrobial agents, herbicides, and antiparasitic agents. Here we investigated the detailed structure-activity relationship of SK from Helicobacter pylori (HpSK). Site-directed mutagenesis and isothermal titration calorimetry studies revealed critical conserved residues (D33, F48, R57, R116, and R132) that interact with shikimate and are therefore involved in catalysis. Crystal structures of HpSK·SO 4, R57A, and HpSK•shikimate-3-phosphate•ADP show a characteristic three-layer architecture and a conformationally elastic region consisting of F48, R57, R116, and R132, occupied by shikimate. The structure of the inhibitor complex, E114A•162535, was also determined, which revealed a dramatic shift in the elastic LID region and resulted in conformational locking into a distinctive form. These results reveal considerable insight into the active-site chemistry of SKs and a selective inhibitor-induced-fit mechanism.

Original languageEnglish
Article numbere33481
JournalPLoS One
Volume7
Issue number3
DOIs
Publication statusPublished - Mar 16 2012
Externally publishedYes

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shikimate kinase
Helicobacter pylori
phosphotransferases (kinases)
Shikimic Acid
shikimate pathway
shikimic acid
antiparasitic agents
Antiparasitic Agents
Aromatic Amino Acids
Mutagenesis
Calorimetry
Phosphorylation
Mammals
Biosynthesis
site-directed mutagenesis
calorimetry
Herbicides
structure-activity relationships
Structure-Activity Relationship
crystal structure

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism. / Cheng, Wen Chi; Chen, Yen Fu; Wang, Hung Jung; Hsu, Kai Cheng; Lin, Shuang Chih; Chen, Tzu Jung; Yang, Jinn Moon; Wang, Wen Ching.

In: PLoS One, Vol. 7, No. 3, e33481, 16.03.2012.

Research output: Contribution to journalArticle

Cheng, Wen Chi ; Chen, Yen Fu ; Wang, Hung Jung ; Hsu, Kai Cheng ; Lin, Shuang Chih ; Chen, Tzu Jung ; Yang, Jinn Moon ; Wang, Wen Ching. / Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism. In: PLoS One. 2012 ; Vol. 7, No. 3.
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