Fig. 6: The transition-state analogue AlF4− can adopt different orientations in diverse P-loop ATPases of the ASCE division. | Nature Communications

Fig. 6: The transition-state analogue AlF4− can adopt different orientations in diverse P-loop ATPases of the ASCE division.

From: Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase

Fig. 6

a AlF4− binding in RecA from E. coli (PDB accession code 3CMW110). The P-loop domain (NBD domain) is shown in orange, the NBD domain of the adjacent activating subunit that provides the stimulating “fingers” is colored yellow. The magnesium ion is shown as a green sphere. To show the catalytic water molecule H2Ocat, the ADP:AlF4− complex is superimposed with the structure of the ADP:AlF4−:H2Ocat complex from the ABC ATPase of the maltose transporter MalK (see PDB accession code 3PUW111). The ADP molecule and AlF4− of MalK are shown in white, H2Ocat as a red sphere, Mg2+ as a teal sphere. ADP moieties were superimposed using atoms O3A, PB and O3B (see Fig. 3b for the atom notation used for ADP) in Pymol112. b Coordination of AlF4− in the BstDnaB structure (see Supplementary Fig. 10, PDB ID 4ESV and ref. 21). The orange, nucleotide-binding chain and the green activating chain correspond to the chains C and B of the 4ESV21. To show the displacement of AlF4−, the GDP:AlF4− complex is superimposed, as described for panel a, with ADP:AlF4− bound to the RecA protein (PDB ID 3CMW, see panel a). The H-bonds formed by AlF4− are shown in blue, the additional interactions that stabilize the position of stimulating sidechains of K418 and R420 are shown in green. The AlF4− moiety is twisted in comparison to the transition-state-mimicking complex shown on panel a. c Coordination of AlF4− in the structure of BstDnaB (see Supplementary Fig. 10, PDB ID 4ESV21). The orange, nucleotide-binding chain and the green activating chain correspond to the chains F and E of the 4ESV PDB structure21. To show the further displacement of AlF4−, the GDP:AlF4− complex of subunit F is superimposed, as described for panel a, with the same complex bound to subunit C of the 4ESV PDB structure21, which is white coloured (see panel b). Bonding interactions that are observed for the GDP:AlF4− complex trapped at the B/C interface (see panel b), but not in this complex trapped at the E/F interface are shown as red dashed lines.

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