7L4S

Crystal structure of the OxyR regulatory domain of Shewanella oneidensis MR-1, reduced form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Functional Irreplaceability of Escherichia coli and Shewanella oneidensis OxyRs Is Critically Determined by Intrinsic Differences in Oligomerization.

Sun, W.Fan, Y.Wan, F.Tao, Y.J.Gao, H.

(2022) mBio 13: e0349721-e0349721

  • DOI: https://doi.org/10.1128/mbio.03497-21

  • PubMed Abstract: 

    LysR-type transcriptional regulators (LTTRs), which function in diverse biological processes in prokaryotes, are composed of a conserved structure with an N-terminal DNA-binding domain (DBD) and a C-terminal signal-sensing regulatory domain (RD). LTTRs that sense and respond to the same signal are often functionally exchangeable in bacterial species across wide phyla, but this phenomenon has not been demonstrated for the H 2 O 2 -sensing and -responding OxyRs. Here, we systematically examined the biochemical and structural determinants differentiating activator-only OxyRs from dual-activity ones by comparing OxyRs from two Gammaproteobacteria , Escherichia coli and Shewanella oneidensis. Our data show that Ec OxyR could function as neither an activator nor a repressor in S. oneidensis. Using So OxyR-based OxyR chimeras and mutants, we demonstrated that residues 283 to 289, which form the first half of the last C-terminal α-helix (α10), are critical for the proper function of So OxyR and cannot be replaced with the Ec OxyR counterpart. Crystal structural analysis reveals that α10 is important for the oligomerization of So OxyR, which, unlike Ec OxyR, forms several high-order oligomers upon DNA binding. As the mechanisms of OxyR oligomerization vary substantially among bacterial species, our findings underscore the importance of subtle structural features in determining regulatory activities of structurally similar proteins descending from a common ancestor. IMPORTANCE Evolution may drive homologous proteins to be functionally nonexchangeable in different organisms. However, much is unknown about the mechanisms underlying this phenomenon beyond amino acid substitutions. Here, we systematically examined the biochemical and structural determinants differentiating functionally nonexchangeable OxyRs, H 2 O 2 -responding transcriptional regulators from two Gammaproteobacteria , Escherichia coli and Shewanella oneidensis. Using So OxyR-based OxyR chimeras and mutants, we demonstrated that residues 283 to 289, which form the first half of the last C-terminal α-helix (α10), are critical for the proper function of So OxyR and cannot be replaced with the Ec OxyR counterpart. Crystal structural analysis reveals that this last helix is critical for formation of high-order oligomers upon DNA binding, a phenomenon not observed with Ec OxyR. Our findings provide a new dimension to differences in sequence and structural features among bacterial species in determining regulatory activities of homologous regulators.


  • Organizational Affiliation

    Institute of Microbiology, College of Life Sciences, Zhejiang Universitygrid.13402.34, Hangzhou, Zhejiang, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator of oxidative stress OxyR
A, B, C, D, E
A, B, C, D, E, F
304Shewanella oneidensis MR-1Mutation(s): 1 
Gene Names: oxyRSO_1328
UniProt
Find proteins for Q8EHA1 (Shewanella oneidensis (strain MR-1))
Explore Q8EHA1 
Go to UniProtKB:  Q8EHA1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EHA1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.193 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.998α = 90
b = 83.998β = 90
c = 185.141γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Robert A. Welch FoundationUnited StatesC-1565
Ministry of Science and Technology (MoST, China)China2018YFA0901300
National Natural Science Foundation of China (NSFC)China41976087
National Natural Science Foundation of China (NSFC)China31930003

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description