5D4Z

Crystal structure of Repressor from Salmonella-temperate phage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Noncanonical DNA-binding mode of repressor and its disassembly by antirepressor

Kim, M.Kim, H.J.Son, S.H.Yoon, H.J.Lim, Y.Lee, J.W.Seok, Y.-J.Jin, K.S.Yu, Y.G.Kim, S.K.Ryu, S.Lee, H.H.

(2016) Proc Natl Acad Sci U S A 113: E2480-E2488

  • DOI: https://doi.org/10.1073/pnas.1602618113
  • Primary Citation of Related Structures:  
    5D4Z, 5D50

  • PubMed Abstract: 

    DNA-binding repressors are involved in transcriptional repression in many organisms. Disabling a repressor is a crucial step in activating expression of desired genes. Thus, several mechanisms have been identified for the removal of a stably bound repressor (Rep) from the operator. Here, we describe an uncharacterized mechanism of noncanonical DNA binding and induction by a Rep from the temperate Salmonella phage SPC32H; this mechanism was revealed using the crystal structures of homotetrameric Rep (92-198) and a hetero-octameric complex between the Rep and its antirepressor (Ant). The canonical method of inactivating a repressor is through the competitive binding of the antirepressor to the operator-binding site of the repressor; however, these studies revealed several noncanonical features. First, Ant does not compete for the DNA-binding region of Rep. Instead, the tetrameric Ant binds to the C-terminal domains of two asymmetric Rep dimers. Simultaneously, Ant facilitates the binding of the Rep N-terminal domains to Ant, resulting in the release of two Rep dimers from the bound DNA. Second, the dimer pairs of the N-terminal DNA-binding domains originate from different dimers of a Rep tetramer (trans model). This situation is different from that of other canonical Reps, in which two N-terminal DNA-binding domains from the same dimeric unit form a dimer upon DNA binding (cis model). On the basis of these observations, we propose a noncanonical model for the reversible inactivation of a Rep by an Ant.


  • Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea; Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Repressor107Salmonella phage SPC32HMutation(s): 0 
Gene Names: repSPC32H_041
UniProt
Find proteins for T1S9Z0 (Salmonella phage SPC32H)
Explore T1S9Z0 
Go to UniProtKB:  T1S9Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1S9Z0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.599α = 89.99
b = 62.497β = 89.97
c = 267.896γ = 72.7
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description