title: Molecular mechanism underlying the interaction of typical Sac10b family proteins with DNA.
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.
authors.affiliation: Ministry of Education Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, People's Republic of China.
authors.forename: Yan-Feng
authors.initials: YF
authors.lastname: Liu
authors.forename: Nan
authors.initials: N
authors.lastname: Zhang
authors.forename: Xi
authors.initials: X
authors.lastname: Liu
authors.forename: Xinquan
authors.initials: X
authors.lastname: Wang
authors.forename: Zhi-Xin
authors.initials: ZX
authors.lastname: Wang
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Chen
authors.forename: Hong-Wei
authors.initials: HW
authors.lastname: Yao
authors.forename: Meng
authors.initials: M
authors.lastname: Ge
authors.forename: Xian-Ming
authors.initials: XM
authors.lastname: Pan
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry*; D001665:Binding Sites; D019641:DNA, Archaeal / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D017014:Methanobacterium / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D019843:Archaeal Proteins; D019641:DNA, Archaeal; D004268:DNA-Binding Proteins