22YZ

Crystal structure of RipNE220A(82-474) from Ralstonia solanacearum

Summary for 22YZ

• Entry DOI: 10.2210/pdb22yz/pdb
• Descriptor: Type III effector protein, GLYCEROL, ACETATE ION, ... (4 entities in total)
• Functional Keywords: nudix effector ralstonia solanacearum, ripn, hydrolase
• Biological source: Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000) (Ralstonia solanacearum)
• Total number of polymer chains: 2
• Total formula weight: 87382.80

Authors

Ge, H. (deposition date: 2026-01-28, release date: 2026-03-11)

Primary citation

Chen, X.,Zhou, Z.,Lu, L.,Xiao, C.,Cao, L.,Cao, Y.,Ge, H.,Wang, W.,Gao, J.
Structural basis of dinucleotide substrate recognition and catalysis by the Nudix effector RipN from Ralstonia solanacearum.
Biochem.Biophys.Res.Commun., 808:153433-153433, 2026

PubMed Abstract: The type III secreted effector RipN from Ralstonia solanacearum is a Nudix hydrolase that suppresses plant immunity by targeting host dinucleotide metabolism. Although RipN preferentially hydrolyzes NADH, the structural basis of its substrate specificity and catalytic mechanism has remained unclear. Here, we report the crystal structures of the full-length RipN and a truncated mutant, RipNΔN81. RipN adopts a Nudix fold featuring a composite substrate-binding pocket formed by the conserved catalytic core and surrounding structural elements. CASTp analysis indicates that this cavity is well suited to accommodate bulky dinucleotide substrates. Molecular docking analyses reveal that NADH, ADP-ribose and FAD share a conserved binding mode centered on the adenosyl diphosphate scaffold, which is coordinated indirectly through Mg ions. We further identify Tyr318 and Glu384 as key substrate-discriminating residues that mediate base-specific interactions and steric exclusion, enabling RipN to efficiently hydrolyze NADH while excluding closely related metabolites such as NADPH and UDP-glucose. Based on structural and docking data, we propose a Glu220-dependent, Mg-assisted catalytic mechanism involving activation of a conserved water molecule for phosphoanhydride bond cleavage. Together, these findings provide mechanistic insight into how RipN selectively targets host dinucleotide metabolites and illustrate how a conserved Nudix scaffold is adapted for effector-specific functions.

PubMed: 41702187
DOI: 10.1016/j.bbrc.2026.153433

Experimental method

X-RAY DIFFRACTION (1.8 Å)