Structural study reveals the temperature-dependent conformational flexibility of Tk-PTP, a protein tyrosine phosphatase from Thermococcus kodakaraensis KOD1
Fig 2
Crystal structure of Tk-PTP(form II).
(A) Tk-PTP(form II) is presented as a secondary structure-labeled ribbon drawing. Cyan, α-helices; navy, β-strands; white, the remaining structures. The catalytic cysteine residue is labeled as C93 and the vanadate molecule bound to the active site pocket is shown in sticks. (B) Stereo views of Cα traces of two forms of Tk-PTP. The P-loop and α4−α5 loop regions are indicated by dotted circles and rectangles, respectively. (C) Stereo views of the superimposed P-loops of two forms of Tk-PTP shown in sticks. For clarity, the main chain and the side chains of Cys93 and Arg99 are shown. Vanadate-mediated hydrogen bonds and electrostatic interactions are presented as dashed lines. Dotted circles indicate the backbone carbonyl of Met94 that undergoes a peptide flip. The GG motif residues are marked with asterisks. A 2Fo-Fc electron density omit map of the vanadate molecule contoured at 1.5 σ is shown together. The temperature factor of vanadate bound to Tk-PTP(form II) is 18.2. (D) Stereo views of the superimposed P-loops of Tk-PTP(form II) and DUSP23a shown in sticks. The PDB code for DUSP23a bound to vanadate is 4ERC. (E) The P-loops of two forms of Tk-PTP are shown in labeled sticks along with the 2Fo-Fc electron density map contoured at 1.5 σ. The direction of main chain amides of four P-loop-constituting central residues are indicated by arrows. (F) The sequences of the P-loop of Tk-PTP and 28 DUSP members are aligned. DUSP1–28 are from human; TbpA is from Pseudomonas aeruginosa; VH1 is from Vaccinia virus. Conserved residues are shaded in green. The PTP signature motif is shown at the top, and the GG motif residues in the P-loop of Tk-PTP are marked in red.