9Z71 | pdb_00009z71

Structure of E. roggenkampii CapS

• PDB DOI: https://doi.org/10.2210/pdb9Z71/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Enterobacter roggenkampii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-11-15 Released: 2026-06-03 
• Deposition Author(s): Chambers, L.R., Corbett, K.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: in silico

Literature

A DNA damage-activated kinase phosphorylates a transcriptional repressor to control bacterial immune pathway expression.

Chambers, L.R., Rani, P., Min, R.K., Villa, E., Corbett, K.D.

(2026) EMBO J 

• PubMed: 42265283 
• DOI: https://doi.org/10.1038/s44318-026-00831-y
• Primary Citation Related Structures: 
  9Z71, 9Z72, 9Z73, 9Z7O


• PubMed Abstract: 
  

  Bacteria encode numerous stress-response pathways that protect their hosts against both internal and external threats. A key question is how these pathways are regulated, especially anti-phage immune pathways that mediate host-cell killing. Here, we identify two proteins termed CapK and CapS that are encoded upstream of diverse immune operons, and regulate these operons' expression in response to DNA damage. CapK resembles bacterial anti-sigma factor kinases, and CapS resembles STAS-domain antagonists of these proteins. CapS is a DNA-binding transcriptional repressor, and phosphorylation of CapS by CapK results in dissociation of a CapS homodimer and de-repression of transcription. The CapK kinase is directly activated by single-stranded DNA generated as a byproduct of DNA repair. Finally, we show that CapK and CapS-like proteins have been co-opted into an anti-phage toxin-antitoxin system with a VapC-like protein, where they similarly respond to DNA damage to activate VapC nuclease activity. Overall, our results reveal how a kinase-substrate pair can regulate expression of an adjacent operon in response to DNA damage, and highlight the modularity of immune and other stress-response pathways.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, University of California San Diego, La Jolla, CA, 92093, USA.
Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA.
Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA.
Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA. [e-mail].
Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.78 kDa 
• Atom Count: 1,599 
• Modeled Residue Count: 182 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Winged helix-turn-helix transcriptional regulator	A	184	Enterobacter roggenkampii	Mutation(s): 0  Gene Names: WP5S18C02_40780
UniProt
Find proteins for A0A443UND6 (Enterobacter cloacae) Explore A0A443UND6  Go to UniProtKB:  A0A443UND6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/1238

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.826	α = 90
b = 55.826	β = 90
c = 184.515	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Chambers, L.R., Corbett, K.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM144121

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release
  
• Version 1.1: 2026-06-24
  Changes: Database references