3FSS

Structure of the tandem PH domains of Rtt106

Summary for 3FSS

• Entry DOI: 10.2210/pdb3fss/pdb
• Descriptor: Histone chaperone RTT106, GLYCEROL, MALONIC ACID, ... (4 entities in total)
• Functional Keywords: histone chaperone, chaperone, chromosomal protein, nucleus, phosphoprotein, transcription, transcription regulation, transposition
• Biological source: Saccharomyces cerevisiae (Baker's yeast, yeast)
• Cellular location: Nucleus: P40161
• Total number of polymer chains: 1
• Total formula weight: 27745.03

Authors

Su, D.,Thompson, J.R.,Mer, G. (deposition date: 2009-01-11, release date: 2009-12-22, Last modification date: 2021-10-20)

Primary citation

Su, D.,Hu, Q.,Li, Q.,Thompson, J.R.,Cui, G.,Fazly, A.,Davies, B.A.,Botuyan, M.V.,Zhang, Z.,Mer, G.
Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106.
Nature, 483:104-107, 2012

PubMed Abstract: Dynamic variations in the structure of chromatin influence virtually all DNA-related processes in eukaryotes and are controlled in part by post-translational modifications of histones. One such modification, the acetylation of lysine 56 (H3K56ac) in the amino-terminal α-helix (αN) of histone H3, has been implicated in the regulation of nucleosome assembly during DNA replication and repair, and nucleosome disassembly during gene transcription. In Saccharomyces cerevisiae, the histone chaperone Rtt106 contributes to the deposition of newly synthesized H3K56ac-carrying H3-H4 complex on replicating DNA, but it is unclear how Rtt106 binds H3-H4 and specifically recognizes H3K56ac as there is no apparent acetylated lysine reader domain in Rtt106. Here, we show that two domains of Rtt106 are involved in a combinatorial recognition of H3-H4. An N-terminal domain homodimerizes and interacts with H3-H4 independently of acetylation while a double pleckstrin-homology (PH) domain binds the K56-containing region of H3. Affinity is markedly enhanced upon acetylation of K56, an effect that is probably due to increased conformational entropy of the αN helix of H3. Our data support a mode of interaction where the N-terminal homodimeric domain of Rtt106 intercalates between the two H3-H4 components of the (H3-H4)(2) tetramer while two double PH domains in the Rtt106 dimer interact with each of the two H3K56ac sites in (H3-H4)(2). We show that the Rtt106-(H3-H4)(2) interaction is important for gene silencing and the DNA damage response.

PubMed: 22307274
DOI: 10.1038/nature10861

Experimental method

X-RAY DIFFRACTION (1.432 Å)