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Figure 3
(a) The active site of PPD1 with bound phosphate. The Fe and Mn atoms are shown as purple and pink spheres, respectively. The average metal–protein ligand distances for the three subunits are Tyr315 1.9 Å, His478 2.2 Å, Asp312 2.3 Å and Asp271 2.1 Å at the Fe site, and His434 2.2 Å, His476 2.2 Å, Asn345 2.1 Å and Asp312 2.3 Å at the Mn site. The phosphate anion is coordinated to both metals via a bridging O atom (Fe/Mn—O distance of ∼2.3 Å). The sixth coordination position of each metal is provided by two of the remaining phosphate O atoms at ∼2.5 Å. The 2Fo − Fc electron-density maps are shown contoured at 1.2σ. (b) The active site of PPD1 (green) and sweet potato PAP (blue). A view is shown from the molecular surface looking into the bimetallic centre, with the conserved metal-ligand residues represented by sticks and the neighbouring, largely nonconserved, active-site residues shown in ball-and-stick representation. The substrate-entry space is larger and more hydrophobic in PPD1 (e.g. Phe286 and Phe444 at the substrate-entry pocket are separated by ∼12 Å, compared with the ∼6 Å separation between His295 and Glu365 in sweet potato PAP), which allows significant differences in substrate accommodation and substrate reactivity (e.g. with bis-pNPP).

IUCrJ
Volume 1| Part 2| February 2014| Pages 101-109
ISSN: 2052-2525
doi:10.1107/S205225251400400X