Document Detail

Secondary structure of the C-terminal DNA-binding domain of the transcriptional activator NifA from Klebsiella pneumoniae: spectroscopic analyses.
MedLine Citation:
PMID:  9882444     Owner:  NLM     Status:  MEDLINE    
The conformation of the C-terminal DNA-binding domain of the transcriptional activator NifA from Klebsiella pneumoniae has been probed by circular dichroism (CD), Fourier-transformed infrared (FT-IR), and nuclear magnetic resonance (NMR) spectroscopy in combination. Secondary structure prediction suggests that the C-terminal half of the domain contains three alpha-helices. The spectra show that the domain is folded in the absence of DNA and of the N-terminal and central domains of NifA. The three spectroscopic techniques suggest slightly different proportions of secondary structural elements but all suggest that it contains about 33% alpha-helix. These results are in agreement with a previous prediction suggesting that NifA contains a helix-turn-helix motif and with the amount of alpha-helix predicted. The environment of the aromatic residues was examined by CD and NMR spectroscopy, which suggest that one or both of the tryptophan residues are involved in the tertiary structure of the protein but that the tyrosine residue in the helix-turn-helix motif is solvent exposed and so available to bind to DNA. The thermal melting profiles and pH-dependent structural changes were also examined by CD spectroscopy. This technique indicates that at low pH there is an increase in the secondary structure and interactions contributing to the tertiary structure. Many of the acidic residues are predicted to be on a single helix, before the helix-turn-helix motif, which may therefore be important for maintaining the structure and function of the C-terminal peptide; alternatively, the N-terminal half of the domain may become more folded at low pH.
S Missaillidis; M Jaseja; P Ray; R Chittock; C W Wharton; A F Drake; M Buck; E I Hyde
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Archives of biochemistry and biophysics     Volume:  361     ISSN:  0003-9861     ISO Abbreviation:  Arch. Biochem. Biophys.     Publication Date:  1999 Jan 
Date Detail:
Created Date:  1999-02-11     Completed Date:  1999-02-11     Revised Date:  2010-08-25    
Medline Journal Info:
Nlm Unique ID:  0372430     Medline TA:  Arch Biochem Biophys     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  173-82     Citation Subset:  IM    
Copyright Information:
Copyright 1999 Academic Press.
Department of Chemistry, University of York, York, United Kingdom.
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MeSH Terms
Amino Acid Sequence
Bacterial Proteins / chemistry*
Binding Sites
Circular Dichroism
DNA / metabolism*
Electrophoresis, Polyacrylamide Gel
Klebsiella pneumoniae / chemistry*
Molecular Sequence Data
Nuclear Magnetic Resonance, Biomolecular
Protein Binding
Protein Conformation
Protein Structure, Secondary
Protein Structure, Tertiary
Sequence Analysis
Spectroscopy, Fourier Transform Infrared
Transcription Factors / chemistry*
Grant Support
//Wellcome Trust
Reg. No./Substance:
0/Bacterial Proteins; 0/NifA protein, Bacteria; 0/Transcription Factors; 9007-49-2/DNA

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