9M80

cryo-EM structure of maltose and glucose bound rice PHS1(R709A)-DPE1(D391A) complex

Summary for 9M80

• Entry DOI: 10.2210/pdb9m80/pdb
• EMDB information: 63699
• Related PRD ID: PRD_900001
• Descriptor: 4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic, Alpha-1,4 glucan phosphorylase, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: complex, starch biosynthersis, rice, maltooligosaccharide elongation, inactive mutant, transferase
• Biological source: Oryza sativa Japonica Group (Japanese rice); More
• Total number of polymer chains: 4
• Total formula weight: 351581.66

Authors

Liu, J.,Yan, J. (deposition date: 2025-03-11, release date: 2026-04-22, Last modification date: 2026-07-22)

Primary citation

Liu, J.,Wu, X.,He, H.,Yang, X.,Hu, Y.,Zhang, F.,Fan, R.,Wang, X.,Yang, S.,Xiong, L.,Zhang, D.,Yin, P.,Guo, J.,Liu, Z.,Yan, J.
The plastidial PHS1-DPE1 complex drives efficient malto-oligosaccharides synthesis in rice starch metabolism.
Nat Commun, 17:-, 2026

PubMed Abstract: Starch serves as a vital energy reserve in plants. During its biosynthesis, malto-oligosaccharides (MOS) are essential primers. One of the key pathways for MOS production involves plastidial α-glucan phosphorylase (PHS1/Pho1) and disproportionating enzyme (DPE1). However, the functional relationship between these enzymes is unclear. Here, we demonstrate that rice PHS1 and DPE1 assemble into a multimeric complex. Cryo-EM structures of the PHS1-DPE1 complex reveal an assembly mechanism and suggest a potential substrate tunnel. Biochemical assays show the complex dramatically enhances catalytic efficiency over individual enzymes. Single-molecule fluorescence resonance energy transfer (smFRET) visualizes conformational dynamics, enabling rapid substrate transfer between the enzymes. We further identify the unique L80 loop in PHS1 as a potential regulator. Its deletion reduces catalytic efficiency and prolongs conformational state lifetimes during substrate transfer, thereby reducing the production of longer MOSs. Our findings establish that the PHS1-DPE1 complex facilitates efficient MOS primer synthesis through efficient substrate transfer or diffusion between the two enzymes, providing mechanistic insight into a critical step of starch biosynthesis with agronomic implications.

PubMed: 42069819
DOI: 10.1038/s41467-026-72738-5

Experimental method

ELECTRON MICROSCOPY (3.07 Å)