Extended Data Fig. 7: Conformational variety of nucleotide binding sites.
From: Dissecting the conformational complexity and mechanism of a bacterial heme transporter
(a) Top panel: closeup view of NBSC conformations in the \({{{\mathbf{Occ}}}}_{{{{\mathrm{return}}}}}^{{{{\mathrm{apo}}}}}\) (ATP), \({{{\mathbf{IF}}}}_{{{{\mathrm{asym}}}}}^{{{{\mathrm{apo}}}}}\) (ADP + Pi), and \({{{\mathbf{IF}}}}_{{{{\mathrm{confined}}}}}^{{{{\mathrm{heme}}}}}\) (apo) states. Distances between the γ-phosphate and S487D (signature loop), and between K379C of the Walker A domain and S487D are indicated by dashed lines. Bottom panel: closeup view of NBSD conformations in the \({{{\mathbf{Occ}}}}_{{{{\mathrm{return}}}}}^{{{{\mathrm{apo}}}}}\) (ATP), \({{{\mathbf{IF}}}}_{{{{\mathrm{asym}}}}}^{{{{\mathrm{apo}}}}}\) (ATP), and \({{{\mathbf{IF}}}}_{{{{\mathrm{confined}}}}}^{{{{\mathrm{heme}}}}}\) (AMP-PNP) states. Distances between the γ-phosphates of ATP/AMP-PNP and S476C of the signature loop are indicated by dashed lines. Conserved structural motifs of nucleotide binding and hydrolysis sites are highlighted. ATP, green; ADP, purple; AMP-PNP, gray; phosphate, orange; Mg2+, yellow. (b-d) Sequence alignments of the CydD and CydC NBDs from E. coli, M. tb, M. smegmatis and B. subtilis revealing the highly conserved motifs for ATP binding and hydrolysis. Highly conserved residues are highlighted in blue. Conserved amino acid groups are highlighted in gray.
