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Figure 2
Structure of YdaT. (a) Cartoon representation of the YdaT monomer (chain A from PDB entry 8bt1, this work). Secondary-structure elements are labelled except for helix α5, which is hidden behind helices α2 and α3. The helix–turn–helix motif is highlighted, with the recognition helix (α3) in red, helix α2 in orange and the connecting loop in yellow. (b) Cartoon representation of the YdaT tetramer with each chain in a distinct colour. The two subunits in shades of green form one functional DNA-binding dimer (chains A and C in PDB entry 8bt1), while the other two subunits in shades of blue (chains B and D) form the second functional DNA-binding dimer. (c) Superposition of the HTH motifs of YdaT [coloured as in (a)] and mouse Oct-4 (blue; PDB entry 6ht5) based on their POU domains (Phillips & Luisi, 2000BB33). The long loop between helices α2 and α3 is absent from Oct-4 and the recognition helix α3 is significantly longer in YdaT compared with Oct-4. (d) Tetramer formation though the creation of a four-helix bundle. In two subunits helix α6 is shown as a cartoon, while in the other two subunits this helix is shown as a grey Cα trace. Side chains that make up the hydrophobic core are shown as sticks. (e) Superposition of the four subunits in the crystal structure of the YdaT tetramer. The tetramerization helices α6 are superimposed, showing the variability in orientation of the corresponding POU domains. The POU domains of chains A and C are coloured green and oriented differently from the POU domains in chains B and D, which are coloured blue.

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ISSN: 2059-7983
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