1X3U

Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium meliloti and its recognition of the fixK promoter

Kurashima-Ito, K.Kasai, Y.Hosono, K.Tamura, K.Oue, S.Isogai, M.Ito, Y.Nakamura, H.Shiro, Y.

(2005) Biochemistry 44: 14835-14844

  • DOI: https://doi.org/10.1021/bi0509043
  • Primary Citation of Related Structures:  
    1X3U

  • PubMed Abstract: 

    FixJ is a response regulator of the two-component signal transduction pathway involved in the transcriptional activation of nitrogen fixation genes of Sinorhizobium meliloti. Upon phosphorylation, FixJ transcriptionally activates the fixK and nifA promoters. We identified a FixJ recognition sequence of 16 bp in the high affinity binding site of the fixK promoter by means of a gel shift assay. In addition, the solution structure of the truncated C-terminal DNA binding domain of FixJ (FixJC) was solved by NMR spectroscopy. FixJC contains five alpha-helices that encode a typical helix-turn-helix motif as a potential DNA binding core with the highest structural similarity toward the C-terminal DNA binding domain of NarL. The addition of the DNA fragment containing the recognition sequence of the high affinity FixJ binding site resulted in intermediate to slow exchange interactions on the NMR time scale in the spectrum of FixJC, while the exchange was rapid in the case of control DNA. These spectral data suggest that more than one molecule of FixJC binds to the recognition sequence, although FixJC alone is present in monomeric form in solution. This result is consistent with a scenario in which a transcriptionally active species of FixJ is a homodimer of the phosphorylated form.


  • Organizational Affiliation

    Yokohama City University, Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein fixJ79Sinorhizobium melilotiMutation(s): 0 
Gene Names: fixJ
UniProt
Find proteins for P10958 (Rhizobium meliloti (strain 1021))
Explore P10958 
Go to UniProtKB:  P10958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10958
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations