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Protein-Nucleic Acid Interaction: Versatile Glutamate

SBKB [doi:10.1038/sbkb.2012.148]
Featured Article - July 2013
Short description: A cyanobacterial transcription factor recognizes three consecutive cytosines in promoter DNA using a single glutamate residue.

Ribbon diagram of sequence-specific recognition in the HetR-DNA complex detailing how Glu71 interacts with three consecutive cytosines. Protein and DNA are colored blue and green, respectively. Figure courtesy of Andrzej Joachimiak.

Nitrogen-fixing cyanobacteria respond to the absence of nitrogen by differentiating specialized cells called heterocysts, in a process regulated by the HetR transcription factor. Joachimiak, Haselkorn and colleagues (PSI MCSG) have solved structures of HetR bound to various DNA target sequences. The 2.50-Å structure of dimeric HetR in complex with a consensus sequence containing distinctive triplets of guanine-cytosine (GC) base pairs (PDB 3QOD) reveals the structural basis of sequence-specific recognition. Compared to HetR in its free state, HetR in this complex is more ordered and symmetric, while the DNA is bent by ∼30° following the curved, positively-charged protein surface. While many direct and solvent-mediated interactions are observed, the main specific binding determinants are contained in the two helix-turn-helix (HTH) motifs that insert symmetrically into the DNA major groove.

Among the many interactions observed were several phosphate contacts on both strands that fix the register of DNA binding; for example α-helix dipole interactions for the three α-helices, exemplified by helix H4 in the major groove, where the positively-charged N-terminus interacts with a phosphate and helical residues engage in backbone and specific side-chain interactions with both protein and DNA. In addition, a unique pattern of base-specific interactions in the major groove is observed for three strictly conserved HTH residues. Strikingly, a glutamate (Glu71) in the turn forms hydrogen bonds with three consecutive cytosines in the GC base pair triplets; a lysine and an arginine make additional interactions with adenine and guanine bases. The two arms of the DNA palindrome show slightly different interactions, suggesting that the structure captures the complex in two states: one in which all contacts are formed and a binding intermediate in which selected water-mediated contacts are present.

Remarkably, substitution of Glu71 with arginine, glutamine or asparagine completely abolishes binding and heterocyst differentiation in vivo, as measured by a complementation assay. Furthermore, structures with longer DNA duplexes revealed possible roles for a flap domain in binding, in addition to a HetR tetramer bound to two duplexes. Since HetR regulates multiple loci, the authors suggest that the tetramer may have a role in coordinated gene expression.

Michael A. Durney


  1. Y Kim et al. Structures of complexes comprised of Fischerella transcription factor HetR with Anabena DNA targets.
    PNAS. 110, E1716-E1723 (2013). doi:10.1073/pnas.1305971110

  2. Y Kim et al. Structure of transcription factor HetR required for heterocyst differentiation in cyanobacteria.
    PNAS. 108, 10109-10114 doi:10.1073/pnas.1106840108

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Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health