9Q2Y | pdb_00009q2y

Phosphodiesterase from Burkholderia phage BCSR5 in the open lid conformation

• PDB DOI: https://doi.org/10.2210/pdb9Q2Y/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Burkholderia phage BCSR5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-15 Released: 2025-11-05 
• Deposition Author(s): Doherty, E.E., Blount, N., Doudna, J.A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: in silico

Literature

Divergent viral phosphodiesterases for immune signaling evasion.

Doherty, E.E., Nomburg, J., Adler, B.A., Lopez, S., Hsieh, K., Price, N., Blount, N., Doudna, J.A.

(2025) Cell Host Microbe 33: 2043-2051.e6

• PubMed: 41297541 
• DOI: https://doi.org/10.1016/j.chom.2025.10.018
• Primary Citation of Related Structures:  
  9Q2G, 9Q2Y


• PubMed Abstract: 
  

  Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to humans. In response, viruses use phosphodiesterase (PDE)-mediated oligonucleotide cleavage for immune evasion, a strategy whose diversity has not yet been explored. Here, we use a canonical 2H PDE (2H PDE) structure-based search of prokaryotic and eukaryotic viral sequences to identify an exceptional diversity of 2H PDEs across the virome, including enzymes not detectable with sequence search methods alone. Despite active site conservation, biochemical experiments reveal remarkable substrate specificity of these PDEs that corresponds to variations in the core 2H fold. This nuanced specificity allows 2H PDEs to selectively degrade oligonucleotide messengers to avoid interfering with host nucleotide signaling. Together, these findings nominate viral 2H PDEs as key regulators of CDN signaling across the tree of life.

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Organizational Affiliation: 
• Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA.
Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94114, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94114, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.95 kDa 
• Atom Count: 2,795 
• Modeled Residue Count: 320 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-CBASS protein Acb1	A, B	165	Burkholderia phage BCSR5	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	C [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.513	α = 90
b = 74.8	β = 90
c = 76.727	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Doherty, E.E., Blount, N., Doudna, J.A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)		--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release
  
• Version 1.1: 2026-01-28
  Changes: Database references