Extended Data Fig. 6: LMNG-like densities in the hydrophobic pocket.
From: Structural basis for the catalytic mechanism of human lipid phosphate phosphatases
a, Functional verification of His31 and Lys161 residues using LPA, PA and S1P as substrates. Data are presented as the means ± s.d. of three independent experiments, each with two technical repeats (n=6). Significant differences were determined with one-way ANOVA with Tukey’s multiple comparisons tests. b, SEC profiles of enzymes with H31A and K161A mutations. c, Some extra densities are observed within a hydrophobic pocket in the vicinity of the catalytic cavity in all four structures. The catalytic and hydrophobic cavities are marked with yellow and red ellipses, respectively. The extra densities in the pocket are contoured at 4σ. Notably, these extra densities in LPP1-C3M align well with an LMNG molecule. d, EM maps of the LMNG molecule are contoured at 3σ. The LMNG molecules are shown as white sticks and balls. e, SEC profiles of LPP1-C3M reconstituted into nanodiscs. The peak fractions were concentrated for cryo-EM sample preparation. Inset: SDS‒PAGE analysis of the concentrated protein used for cryo-EM sample preparation. f, Map overlay of LPP1-C3M structures in detergent and nanodisc environments. Insets: Zoomed-in views to show the extra densities at the catalytic cavities of LPP1-C3M in detergent and nanodisc environments. Both MAG and LMNG molecules are absent in the LPP1-C3M structure in the nanodisc.
