Structure-based stability analysis of an extremely stable dimeric DNA binding protein from Sulfolobus islandicus.

ORF56 is a small and thermodynamically extremely stable dimeric protein from the archaeon Sulfolobus islandicus. This DNA binding protein is encoded on plasmid pRN1 and possibly controls the copy number of the plasmid. We report the solution NMR structure as well as the crystal structure of ORF56 comprising a ribbon−helix−helix fold. The homodimer consists of an antiparallel intersubunit β-sheet and two α-helices per monomer, which is a common DNA binding fold of plasmid- and phage-encoded gene regulation proteins. NMR titration experiments with ORF56 and double-stranded DNA derived from its promoter binding site revealed that it is largely the β-sheets that interact with the DNA. The β-sheet experiences high local fluctuations, which are conserved among DNA binding ribbon−helix−helix dimers from mesophilic and hyperthermophilic organisms. In contrast, residues strongly protected against H−D exchange are localized in helix 2, forming the hydrophobic intermolecular core of the dimer. A structure-based comp...