Structure of Alba: an archaeal chromatin protein modulated by acetylation

Abstract

contributed equally to this work Eukaryotic DNA is packaged into nucleosomes that regulate the accessibility of the genome to replication, transcription and repair factors. Chromatin accessibility is controlled by histone modi®cations including acetylation and methylation. Archaea possess eukaryotic-like machineries for DNA replication, transcription and information processing. The conserved archaeal DNA binding protein Alba (formerly Sso10b) interacts with the silencing protein Sir2, which regulates Alba's DNA binding af®nity by deacetylation of a lysine residue. We present the crystal structure of Alba from Sulfolobus solfataricus at 2.6 A Ê resolution (PDB code 1h0x). The fold is reminiscent of the N-terminal DNA binding domain of DNase I and the C-terminal domain of initiation factor IF3. The Alba dimer has two extended b-hairpins¯anking a central body containing the acetylated lysine, Lys16, suggesting three main points of contact with the DNA. Fluorescence, calorimetry and electrophoresis data suggest a ®nal binding stoichiometry of~5 bp DNA per Alba dimer. We present a model for the Alba±DNA interaction consistent with the available structural, biophysical and electron microscopy data.

Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic ArchaeonPyrococcus horikoshiiOT3

“…It is known that SsoAlba is an = protein consisting of two -helices and four -strands, 25) and that the Pyrococcus proteins are generally thermostable. To evaluate the structural integrity and also to confirm thermostability of the resulting protein, PhoAlba, we measured circular dichroism (CD) spectrum at 37 C in the far-ultraviolet region (200 nm-250 nm), where the spectra reflects the content of the secondary structures of the protein.…”

“…The crystal structure of PhoAlba was determined by the molecular replacement method using S. solfataricus Alba (SsoAlba) 25) as a search model with program CNS. 27) Structure refinement was done using CNS with diffraction data from 50.0 to 2.8 Å resolution.…”

“…Based on the crystal structures of SsoAlba1 and SsoAlba2, models for the Alba proteins bound to both B-DNA and A-DNA (or RNA) have been proposed. 25,34) In these models, the two loops between 1 and 1 in the dimer bind to the phosphates across the major groove of DNA or RNA, whereas the two flexible hairpin arms between 3 and 4 in the dimer extend from the body in the opposite direction oriented to contact the minor groove of DNA or RNA. The loop between 1 and 1 and -hairpin loop between 3 and 4 in PhoAlba are highly conserved with the corresponding structures in other Alba proteins.…”

“…2,3) Hence it was referred to as PhoAlba. In this study, to provide further structural information about euryarchaeal Alba proteins, we determined the crystal structure of PhoAlba at a resolution of 2.8 Å with molecular replacement using, the Alba structure (SsoAlba) of S. solfataricus 25) as a search model. We found that PhoAlba has a topology similar to archaeal homologs from euryarchaeota as well as crenarchaeota.…”

The Archaeal Sac10b Protein Family: Conserved Proteins with Divergent Functions

“…The DNA binding of one member of the Sac10b protein family, Sso10b or Alba, is regulated by acetylation (Alba: acetylation lowers binding affinity); the acetyltransferase Pat specifically acetylates Alba on Lys16 thereby lowering the affinity for DNA [25] whereas removal of the acetyl group is catalyzed by an archaeal homologue of the deacetylase Sir2 resulting in transcriptional repression [26]. Alba was the first Sac10b family protein whose highresolution structure was determined by X-ray crystallography and for which a model of its interaction with DNA was proposed [27]. Meanwhile the structures of further hyperthermophilic archaeal proteins of the Sac10b family were solved by X-ray crystallography and/or NMR spectroscopy [28][29][30][31][32][33][34][35].…”