1: J Biol Chem. 2007 Apr 20;282(16):11921-30. Epub 2007 Feb 28.

The N-terminal extensions of Deinococcus radiodurans Dps-1 mediate DNA major
groove interactions as well as assembly of the dodecamer.

Bhattacharyya G, Grove A.

Department of Biological Sciences, Louisiana State University, Baton Rouge,
Louisiana 70803, USA.

Dps (DNA protection during starvation) proteins play an important role in the
protection of prokaryotic macromolecules from damage by reactive oxygen species. 
Previous studies have suggested that the lysine-rich N-terminal tail of Dps
proteins participates in DNA binding. In comparison with other Dps proteins,
Dps-1 from Deinococcus radiodurans has an extended N terminus comprising 55 amino
acids preceding the first helix of the 4-helix bundle monomer. In the crystal
structure of Dps-1, the first approximately 30 N-terminal residues are invisible,
and the remaining 25 residues form a loop that harbors a novel metal-binding
site. We show here that deletion of the flexible N-terminal tail obliterates
DNA/Dps-1 interaction. Surprisingly, deletion of the entire N terminus also
abolishes dodecameric assembly of the protein. Retention of the N-terminal metal 
site is necessary for formation of the dodecamer, and metal binding at this site 
facilitates oligomerization of the protein. Electrophoretic mobility shift assays
using DNA modified with specific major/minor groove reagents further show that
Dps-1 interacts through the DNA major groove. DNA cyclization assays suggest that
dodecameric Dps-1 does not wrap DNA about itself. A significant decrease in DNA
binding affinity accompanies a reduction in duplex length from 22 to 18 bp, but
only for dodecameric Dps-1. Our data further suggest that high affinity DNA
binding depends on occupancy of the N-terminal metal site. Taken together, the
mode of DNA interaction by dodecameric Dps-1 suggests interaction of two
metal-anchored N-terminal tails in successive DNA major grooves, leading to DNA
compaction by formation of stacked protein-DNA layers.

Publication Types: 
    Research Support, U.S. Gov't, Non-P.H.S.

PMID: 17331944 [PubMed - indexed for MEDLINE]