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 1.1 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: 10.1073/pnas.1602618113
  • Structures With Same Primary Citation

  • 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 re ...

    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 Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; sangryu@snu.ac.kr hyungholee@snu.ac.kr.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Repressor1, 2, 3, 4, 5, 6, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, T, U, V, W, X, Y, Z107Salmonella phage SPC32HMutation(s): 0 
Gene Names: repSPC32H_041
Find proteins for T1S9Z0 (Salmonella phage SPC32H)
Explore T1S9Z0 
Go to UniProtKB:  T1S9Z0
Protein Feature View
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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 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references