Abstract
The Sac10b protein family is regarded as a family of DNA-binding proteins that is highly conserved and widely distributed within the archaea. Sac10b family members are typically small basic dimeric proteins that bind to DNA with cooperativity and no sequence specificity and are capable of constraining DNA negative supercoils, protecting DNA from Dnase I digestion, and do not compact DNA obviously. However, a detailed understanding of the structural basis of the interaction of Sac10b family proteins with DNA is still lacking. Here, we determined the crystal structure of Mth10b, an atypical member of the Sac10b family from Methanobacterium thermoautotrophicum ΔH, at 2.2 Å. Unlike typical Sac10b family proteins, Mth10b is an acidic protein and binds to neither DNA nor RNA. The overall structure of Mth10b displays high similarity to its homologs, but three pairs of conserved positively charged residues located at the presumed DNA-binding surface are substituted by non-charged residues in Mth10b. Through amino acids interchanges, the DNA-binding ability of Mth10b was restored successfully, whereas the DNA-binding ability of Sso10b, a typical Sac10b family member, was weakened greatly. Based on these results, we propose a model describing the molecular mechanism underlying the interactions of typical Sac10b family proteins with DNA that explains all the characteristics of the interactions between typical Sac10b family members and DNA.
Highlights
The Sac10b protein family, named Alba, is generally regarded as a family of DNA-binding proteins that are highly conserved and widely distributed within the archaea [1,2,3,4]
We propose a novel model describing the molecular mechanism underlying the interactions of typical Sac10b family proteins with DNA which explains all the characteristics of the interactions between typical Sac10b family proteins and DNA
Each monomer in the Mth10b structure contains four salt bridges: Glu31-Arg89, Lys35-Glu85, Arg37-Glu69, and Glu49-Arg52. These salt bridges are all located on the convex surface of the dimer and may play an important role in bracing and stabilizing the structure, as salt bridge interactions are considered critical for the stability of thermophilic proteins [24,25]
Summary
The Sac10b protein family, named Alba, is generally regarded as a family of DNA-binding proteins that are highly conserved and widely distributed within the archaea [1,2,3,4]. Typical Sac10b family members, such as Sac10b from Sulfolobus acidocaldarius [5,6,7], Ssh10b from S. shibatae [8,9,10,11,12], Sso10b and Sso10b2 from S. solfataricus [13,14,15,16,17,18], Mja10b from Methanocaldococcus jannaschii [19], and Afu10b from Archaeoglobus fulgidus [20], are small basic dimeric proteins which bind to DNA with cooperativity and no apparent sequence specificity. Wardleworth et al first proposed a model for the interaction of Sso10b with the DNA duplex [14]
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