Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY

Shivesh Kumar, Yan Wang, Ye Zhou, Lucas Dillard, Fay-Wei Li, Carly A. Sciandra, Ning Sui, Rodolfo Zentella, Emily Zahn, Jeffrey Shabanowitz, Donald F. Hunt, Mario J. Borgnia, Alberto Bartesaghi (), Tai-ping Sun () and Pei Zhou ()
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Shivesh Kumar: Duke University School of Medicine
Yan Wang: Duke University
Ye Zhou: Duke University
Lucas Dillard: National Institute of Environmental Health Sciences
Fay-Wei Li: Cornell University
Carly A. Sciandra: Duke University School of Medicine
Ning Sui: Duke University
Rodolfo Zentella: Duke University
Emily Zahn: University of Virginia
Jeffrey Shabanowitz: University of Virginia
Donald F. Hunt: University of Virginia
Mario J. Borgnia: National Institute of Environmental Health Sciences
Alberto Bartesaghi: Duke University School of Medicine
Tai-ping Sun: Duke University
Pei Zhou: Duke University School of Medicine

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: Abstract SPINDLY (SPY) in Arabidopsis thaliana is a novel nucleocytoplasmic protein O-fucosyltransferase (POFUT), which regulates diverse developmental processes. Sequence analysis indicates that SPY is distinct from ER-localized POFUTs and contains N-terminal tetratricopeptide repeats (TPRs) and a C-terminal catalytic domain resembling the O-linked-N-acetylglucosamine (GlcNAc) transferases (OGTs). However, the structural feature that determines the distinct enzymatic selectivity of SPY remains unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of SPY and its complex with GDP-fucose, revealing distinct active-site features enabling GDP-fucose instead of UDP-GlcNAc binding. SPY forms an antiparallel dimer instead of the X-shaped dimer in human OGT, and its catalytic domain interconverts among multiple conformations. Analysis of mass spectrometry, co-IP, fucosylation activity, and cryo-EM data further demonstrates that the N-terminal disordered peptide in SPY contains trans auto-fucosylation sites and inhibits the POFUT activity, whereas TPRs 1–5 dynamically regulate SPY activity by interfering with protein substrate binding.

Date: 2023
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DOI: 10.1038/s41467-023-37279-1

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