PLD3 8V05: BI3323-Aug2025

From Proteopedia

Revision as of 14:48, 30 November 2025

Introduction

Phospholipase D3 (PLD3) is an enzyme found inside endolysosomes, where it helps clear out stray single-stranded DNA and RNA before they can trigger immune alarms. The structure shown here (PDB 8V05) represents the soluble luminal portion of mouse PLD3, which closely reflects the behaviour of human PLD4. The crystal structure of mouse PLD3 (PDB ID: 8V05) reveals a pseudo-dimeric architecture consisting of two structurally similar domains, Domain A (residues 69–254) and Domain B (residues 277–488), connected by a flexible linker (residues 255–276). Both domains contain β-sheets. In the first image (Overall Structure), domain A is marked with green and domain B with orange, with a pink linker bridging them. Their interface is involved in catalysis.

Structural highlights

PLD3 uses two conserved HKD motifs to break down genetic material. The first motif (H199, K201, D206) lies in Domain A, and the second (H414, K416, E421) sits in Domain B. Together, they build a positively charged pocket that draws in the negatively charged phosphates of DNA/RNA. Evidence from structural studies suggests that H414 performs the key attack on the phosphodiester bond, briefly forming a phosphohistidine intermediate. H199 from Domain A serves as a proton shuttle, facilitates hydrolysis of this intermediate by activating a water molecule, releasing a single 3′-phosphate nucleotide and regenerating the enzyme. PLD3 also exhibits weak phosphatase activity toward 5′-phosphorylated nucleic acids, whereby H414 captures the 5′ phosphate to form the phosphohistidine intermediate, which is subsequently hydrolyzed to release inorganic phosphate. This phosphatase activity inhibits exonuclease function by trapping the enzyme in the covalent intermediate state. The second image (Active Site) highlights the HKD1 in blue and HKD2 in red.

Significance

PLD3 is an endolysosomal nuclease linked to neuronal health and late-onset Alzheimer’s disease. Its dysfunction leads to impaired nucleic-acid clearance and lysosomal stress. The high-resolution structure of PLD3 (8V05) reveals how its HKD motifs assemble into an active nuclease and how substrates are positioned for cleavage. This structural insight helps explain the effects of disease-associated mutations and supports the development of targeted modulators that influence lysosomal function and neurodegeneration.

References

Meng Yuan, Linghang Peng, Deli Huang, Amanda Gavin, Fangkun Luan, Jenny Tran, Ziqi Feng, Xueyong Zhu, Jeanne Matteson, Ian A. Wilson, and David Nemazee, Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4

3D Images

Overall structure of PLD3 (PDB 8V05).

HKD catalytic center of PLD3.