2K1N

DNA bound structure of the N-terminal domain of AbrB


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into the Nature of DNA Binding of AbrB-like Transcription Factors

Sullivan, D.M.Bobay, B.G.Kojetin, D.J.Thompson, R.J.Rance, M.Strauch, M.A.Cavanagh, J.

(2008) Structure 16: 1702-1713

  • DOI: https://doi.org/10.1016/j.str.2008.08.014
  • Primary Citation of Related Structures:  
    2K1N, 2RO3, 2RO4, 2RO5

  • PubMed Abstract: 

    Understanding the DNA recognition and binding by the AbrB-like family of transcriptional regulators is of significant interest since these proteins enable bacteria to elicit the appropriate response to diverse environmental stimuli. Although these "transition-state regulator" proteins have been well characterized at the genetic level, the general and specific mechanisms of DNA binding remain elusive. We present RDC-refined NMR solution structures and dynamic properties of the DNA-binding domains of three Bacillus subtilis transition-state regulators: AbrB, Abh, and SpoVT. We combined previously investigated DNase I footprinting, DNA methylation, gel-shift assays, and mutagenic and NMR studies to generate a structural model of the complex between AbrBN(55) and its cognate promoter, abrB8. These investigations have enabled us to generate a model for the specific nature of the transition-state regulator-DNA interaction, a structure that has remained elusive thus far.


  • Organizational Affiliation

    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AbrB family transcriptional regulatorC [auth A],
D [auth B],
E [auth C],
F [auth D]
55Bacillus subtilisMutation(s): 0 
Gene Names: B4122_4520B4417_1778DFO69_4335FAL52_19720SC09_Contig28orf00381
UniProt
Find proteins for P08874 (Bacillus subtilis (strain 168))
Explore P08874 
Go to UniProtKB:  P08874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08874
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (25-MER)A [auth E]25synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (25-MER)B [auth F]25synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary