PLD3 8V05: BI3323-Aug2025

From Proteopedia

Revision as of 13:33, 30 November 2025

Summary

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. 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. Mutations that weaken PLD3’s structure or activity are linked to inflammatory and neurodegenerative disorders.

BI3323-Aug2025

3D Scenes

Template:Mrignaki PLD3 8V05:Overall Structure Template:Mrignaki PLD3 8V05:Active Site

3D Images

Overall structure of PLD3 (PDB 8V05).

HKD catalytic center of PLD3.

Scripts

For the overall structure:
load https://files.rcsb.org/download/8V05.pdb

# Display the entire protein as ribbon structure
select protein
cartoon on

# Explicitly hide sticks for all protein residues to ensure no sticks appear in domain regions
select protein
hide sticks

# Color the domains
select 69-254
color green
select 277-488
color orange
select 255-276
color pink

# Show ball-and-stick representation ONLY for the active site residues
select 199,201,206,414,416,421
show sticks
spacefill 100%

# Color the active site residues to distinguish which domain they belong to
select 199,201,206
color blue

select 414,416,421
color red

# Add labels to the most important catalytic histidines
select 199
label "H199" 

# Set all labels to white for better visibility
color labels white

select 414
label "H414"

# Set all labels to white for better visibility
color labels white

# Center the view on the active site
center 199,414
zoom 120

For the active sites only:

load https://files.rcsb.org/download/8V05.pdb

# Explicitly show the protein first, then selectively hide other regions
show protein

# Hide everything except the regions containing the catalytic sites
hide not (190-220 or 405-435)

# Show the selected regions as sticks
select 190-220 or 405-435
show sticks

# Make the key catalytic residues more prominent with larger spheres
select 199, 201, 206, 414, 416, 421
spacefill 150%

# Color the catalytic residues from the two HKD motifs differently
select 199, 201, 206
color blue

select 414, 416, 421
color red

# Add labels to the key catalytic histidines
select 199
label "H199"

# Set all labels to white for better visibility
color labels white


select 414
label "H414"

# Set all labels to white for better visibility
color labels white

# Center the view on the active site
center 199, 414
zoom 120