6JQ1

Crystal Structure of DdrO from Deinococcus geothermalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO.

Lu, H.Wang, L.Li, S.Pan, C.Cheng, K.Luo, Y.Xu, H.Tian, B.Zhao, Y.Hua, Y.

(2019) Nucleic Acids Res 47: 9925-9933

  • DOI: 10.1093/nar/gkz720
  • Primary Citation of Related Structures:  
    6JQ1

  • PubMed Abstract: 
  • DdrO is an XRE family transcription repressor that, in coordination with the metalloprotease PprI, is critical in the DNA damage response of Deinococcus species. Here, we report the crystal structure of Deinococcus geothermalis DdrO. Biochemical and structural studies revealed the conserved recognizing α-helix and extended dimeric interaction of the DdrO protein, which are essential for promoter DNA binding ...

    DdrO is an XRE family transcription repressor that, in coordination with the metalloprotease PprI, is critical in the DNA damage response of Deinococcus species. Here, we report the crystal structure of Deinococcus geothermalis DdrO. Biochemical and structural studies revealed the conserved recognizing α-helix and extended dimeric interaction of the DdrO protein, which are essential for promoter DNA binding. Two conserved oppositely charged residues in the HTH motif of XRE family proteins form salt bridge interactions that are essential for promoter DNA binding. Notably, the C-terminal domain is stabilized by hydrophobic interactions of leucine/isoleucine-rich helices, which is critical for DdrO dimerization. Our findings suggest that DdrO is a novel XRE family transcriptional regulator that forms a distinctive dimer. The structure also provides insight into the mechanism of DdrO-PprI-mediated DNA damage response in Deinococcus.


    Organizational Affiliation

    MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator, XRE familyA, B132Deinococcus geothermalis DSM 11300Mutation(s): 0 
Gene Names: Dgeo_0336
UniProt
Find proteins for Q1J1J5 (Deinococcus geothermalis (strain DSM 11300 / AG-3a))
Explore Q1J1J5 
Go to UniProtKB:  Q1J1J5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1J1J5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.95α = 90
b = 127.9β = 90
c = 156.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31870051

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references