Fig. 5: Crystal structure of the RutR AcK52•uracil complex (PDB ID: 6Z1B). | Nature Communications

Fig. 5: Crystal structure of the RutR AcK52•uracil complex (PDB ID: 6Z1B).

From: Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism

Fig. 5

a Overview of the RutR AcK52•uracil structure in cartoon representation. RutR is an all-helical protein consisting of an N-terminal domain encompassing helices α1-α3 containing the HTH-motif (α2-α3) needed for DNA-binding and a C-terminal ligand-binding domain (LBD), encompassing α-helices α4-α10. A short α-helix, α9, connects α8 and α10, as described for the non-acetylated structure (PDB: 4JYK). RutR forms a dimer with one uracil-molecule bound to the LBD in each monomer. Grey: chain A; blue: chain B (dark color: DNA-binding domain, light color: ligand-binding domain). Acetyl-L-lysine 52 of both chains is shown as stick-representation in green. Upper closeup: The uracil binding site in RutR AcK52. Uracil (green) forms hydrogen bonds with side chains of Q171 (below W167) and a bridging water molecule (red sphere) bound to Y97 of chain A (CA; grey). W167 and W77 form stacking interactions with uracil on both sides of the pyrimidine ring. Uracil is in hydrogen contact distance to Q179’ of the other monomer (chain B, CB: blue). The K52-acetylation does not directly interfere with uracil binding. Shown in blue is the 2Fo-Fc electron density map contoured at 1σ. Lower closeup: of the 2Fo-Fc electron density in blue contoured at 1σ obtained for the acetyl-L-lysine (AcK52) and the neighboring residues S51 and T53 from chain A (CA) of the RutR AcK52•uracil structure presented here (PDB: 6Z1B). b K52-acetylation in RutR abolishes DNA binding exerting a steric and electrostatic mechanism. Upper panel: Superposition of the HTH-motif from the structure of the TetR-repressor QacR in complex with IR1 operator DNA (PDB: 1JT0) and RutR AcK52•uracil (PDB: 6Z1B)84. Both HTH-regions (QacR: aa4-50; RutR aa19-66) superpose well with r.m.s.d. value of 0.83 for C-alpha atoms. closeup: AcK52 (green) electrostatically and sterically affects dsDNA binding. The N-(ε)-amino group of K36 in QacR is in interaction distance to N7 of a guanine base (2.6 Å; red dashed line) creating sequence specificity. This interaction is abolished by K52-acetylation in RutR. A model of RutR in compex with the carAB promoter suggests that K52 interacts with the guanine base at analogous position20. dark brown: HTH-motif from QacR; bright brown: HTH-motif from RutR.

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