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Results: 3

1.
Fig. 3.

Fig. 3. From: Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.

Electrostatic surface potential of TruB. The protein surfaces are colored by their electrostatic potentials, from red (–10 kT) to blue (+10 kT). (A) The front and back surfaces of apo TruB. (B) The front surface of apo TruB with 17-base RNA (shown in green with U55 in magenta) docked into the active site and the view 90° away. (C) The front surface of tmTruB with bound RNA substrate and the view 90° away. The RNA molecules A, B, and C are shown in green, yellow, and blue, respectively. The figure was prepared by using grasp (28).

Hu Pan, et al. Proc Natl Acad Sci U S A. 2003 October 28;100(22):12648-12653.
2.
Fig. 2.

Fig. 2. From: Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.

Protein–RNA interactions and conformational changes on RNA binding. (A) Schematic representation of protein–RNA interactions. Ψ55 is highlighted with red, and the backbones of the RNA molecules A, B, and C are shown in blue, yellow, and green, respectively. Water-mediated contacts are shown in dashed blue lines, directed interactions to the RNA bases are shown in dashed red lines, interactions to the RNA backbones are shown in dashed black lines, and stacking interactions are shown in dashed green lines. (B) Superposition of E. coli apo TruB (yellow), tmTruB–RNA complex (gray), and E. coli TruB–RNA complex (cyan) (14). (C) Interactions between the three flipped-out bases and the protein residues. Hydrogen bonds are shown as green dashed lines, and hydrophobic interactions are shown as red “eyelashes.” The figure was generated by using the program ligplot (27). (D) Detailed view of the specific protein–RNA interactions. (E) Superposition of the T arm bound to TruB (lavender) with corresponding residues from the structure of tRNAPhe (acceptor stem shown in green, D loop shown in blue). (F) Superposition of the catalytic residues of apo TruB (yellow) and the corresponding residues from tmTruB–RNA complex (blue).

Hu Pan, et al. Proc Natl Acad Sci U S A. 2003 October 28;100(22):12648-12653.
3.
Fig. 1.

Fig. 1. From: Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.

Mechanism of Ψ synthases and overall structure of TruB with and without RNA bound. (A) Mechanism proposed for Ψ synthases (25). R represents H or F. If R = F, a stable covalent intermediate is expected. However, in the crystal structure, a hydrolyzed product analogue was observed. (B) Overall structure of apo TruB. The catalytic domain is shown in red, and the C-terminal domain is shown in blue. Residues 124–152 are disordered and indicated by a dotted line. Catalytic residue Asp-48 is shown in green. (C) Overall structure of the tmTruB–RNA complex. The color scheme for the protein part is the same as in B. The thumb loop is in magenta. The three pieces of RNA are as follows: molecule A in cyan, molecule B in yellow, and molecule C in green. U55 is shown in orange. These and other similar illustrations were generated by using ribbons (26).

Hu Pan, et al. Proc Natl Acad Sci U S A. 2003 October 28;100(22):12648-12653.

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