5CLV

Crystal Structure of KorA-operator DNA complex (KorA-OA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator.

Rajasekar, K.V.Lovering, A.L.Dancea, F.Scott, D.J.Harris, S.A.Bingle, L.E.Roessle, M.Thomas, C.M.Hyde, E.I.White, S.A.

(2016) Nucleic Acids Res 44: 4947-4956

  • DOI: https://doi.org/10.1093/nar/gkw191
  • Primary Citation of Related Structures:  
    2N5G, 5CKT, 5CLV, 5CM3

  • PubMed Abstract: 

    The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting cooperatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-amino acid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerization domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20-bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, nuclear magnetic resonance spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in cooperative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerization domain of the tumour suppressor p53.


  • Organizational Affiliation

    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TrfB transcriptional repressor protein
A, B
96Escherichia coliMutation(s): 0 
Gene Names: trfBkorA
UniProt
Find proteins for P03052 (Escherichia coli)
Explore P03052 
Go to UniProtKB:  P03052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03052
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TrfB transcriptional repressor protein
E, F, I, J, M
E, F, I, J, M, N
65Escherichia coliMutation(s): 0 
Gene Names: trfBkorA
UniProt
Find proteins for P03052 (Escherichia coli)
Explore P03052 
Go to UniProtKB:  P03052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03052
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP*GP*GP*)-3'
C, D, G, H, K
C, D, G, H, K, L, O, P
20Escherichia coli
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.280 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.46α = 90
b = 114.03β = 99.59
c = 82.07γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2019-09-11
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description