Fig. 4: Nucleotide and substrate binding to Pdr5.

The panels illustrate the contacts between Pdr5 with (a–d) nucleotides and (e) rhodamine 6 G. Some of the residues that are important for nucleotide binding and/or catalysis are highlighted and labelled (cf. Supplementary Fig. 10). The domain colouring follows the scheme of the previous figure. a The catalytic site (NBS2) of Pdr5 in inward-facing conformation (ADP-Pdr5) with bound ADP. b The catalytic site of outward-facing Pdr5 (AOV-Pdr5) in a vanadate-trapped state that mimics the intermediate step of hydrolysis with an ADP-orthovanadate molecule. A co-ordinated magnesium ion is depicted as a green sphere. c The deviant, inactive site (NBS1) of Pdr5 in the inward-facing conformation (ADP-Pdr5), showing the bound ATP. d The same site in the outward-facing conformation (AOV-Pdr5), The residues surrounding the nucleotide are at the corresponding positions of the catalytic site. e Side view and cross-section of the transmembrane part of Pdr5 in inward-facing conformation (Pdr5-R6G). Dotted line on the side-view denotes the position of the cross-section. The efflux substrate rhodamine 6G is bound in the entrance cavity between TMD1 and TMD2 . The cross-section of Pdr5 is coloured by hydrophobicity, from turquoise (hydrophilic) to tan (most hydrophobic), and electrostatic potential, from red (negative) to blue (positive). Abbreviations: AOV, ADP-orthovanadate; R6G, rhodamine 6G; TMD, transmembrane domain.