Crystal structure of Deinococcus geothermalis PprI complexed with ssDNA

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report

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The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA.

Lu, H.Chen, Z.Xie, T.Zhong, S.Suo, S.Song, S.Wang, L.Xu, H.Tian, B.Zhao, Y.Zhou, R.Hua, Y.

(2024) Nat Commun 15: 1892-1892

  • DOI: https://doi.org/10.1038/s41467-024-46208-9
  • Primary Citation of Related Structures:  
    8SLM, 8SLN

  • PubMed Abstract: 

    Bacteria have evolved various response systems to adapt to environmental stress. A protease-based derepression mechanism in response to DNA damage was characterized in Deinococcus, which is controlled by the specific cleavage of repressor DdrO by metallopeptidase PprI (also called IrrE). Despite the efforts to document the biochemical, physiological, and downstream regulation of PprI-DdrO, the upstream regulatory signal activating this system remains unclear. Here, we show that single-stranded DNA physically interacts with PprI protease, which enhances the PprI-DdrO interactions as well as the DdrO cleavage in a length-dependent manner both in vivo and in vitro. Structures of PprI, in its apo and complexed forms with single-stranded DNA, reveal two DNA-binding interfaces shaping the cleavage site. Moreover, we show that the dynamic monomer-dimer equilibrium of PprI is also important for its cleavage activity. Our data provide evidence that single-stranded DNA could serve as the signal for DNA damage sensing in the metalloprotease/repressor system in bacteria. These results also shed light on the survival and acquired drug resistance of certain bacteria under antimicrobial stress through a SOS-independent pathway.

  • Organizational Affiliation

    MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zn dependent hydrolase fused to HTH domain, IrrE ortholog291Deinococcus geothermalis DSM 11300Mutation(s): 0 
Gene Names: Dgeo_0395
Find proteins for Q1J1D6 (Deinococcus geothermalis (strain DSM 11300 / AG-3a))
Explore Q1J1D6 
Go to UniProtKB:  Q1J1D6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1J1D6
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (29-MER)B [auth D]29synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.99α = 90
b = 84.99β = 90
c = 88.55γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870051

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release