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Figure 1
The crystal structure of PPD1. (a) The PPD1 asymmetric unit is a trimer, shown as a cartoon coloured by individual subunits, with their N- and C-­terminal ends indicated. The metal atoms in each subunit are shown as pink (Mn) and purple (Fe) spheres, with the bound phosphate ligands depicted as sticks. The active sites are 54 Å apart. Disulfides are shown as yellow spheres and sugar groups as silver and red sticks; there are five of each per subunit (one is occluded in the figure). The cysteines or disulfide bridges labelled 1 (Cys577–Cys582), 2 (Cys484–Cys491) and 3 (Cys396–Cys417) constrain flexible loops and help to position the interfacing residues, while that labelled 4 (Cys202–Cys366) is involved in hydrogen bonding to the adjacent subunit. Disulfide bridge 5 (Cys69–Cys82) bridges an extended loop (or turn) in the N-terminal domain and orients it towards the solvent channel above the active site. The sugars are covalently bound to Asn residues 92, 241, 292, 502 and 525. For clarity, water molecules have been omitted. (b) Cartoon representation of the superposition, using secondary-structure matching (SSM) in three dimensions (Krissinel & Henrick, 2004aBB24), of PPD1 (red) with a sweet potato PAP (blue) subunit taken from PDB entry 1xzw (Schenk et al., 2005BB47). The metal atoms are shown as spheres. The alignment of 353 residues gave an overall r.m.s.d. of 1.58 Å between the two structures, with a Z-score of 17.9, and identified the extent of the PAP domain. The C-­terminal end of PPD1, which is 19 residues longer than in sweet potato PAP, extends into the active-site cavity of the neighbouring subunit of the trimer. The fibronectin type III domain identified by Tsyguelnaia & Doolittle (1998BB57) for red kidney bean PAP is also present in sweet potato and PPD1, and is located at the lower centre of the figure. The N-terminal end comprising residues 1–150 is unique to PPD1 and is not part of the known PAP family. (c) The PPD1 hexamer generated from crystallographic symmetry, showing views along and perpendicular to the trimeric axis. (d) The trimer–trimer interface. The active sites are positioned in the interior of the hexamer, approximately 38 Å apart, with 12 intersubunit hydrogen-bonding interactions located at each of the interfaces, directly between the active sites. The residues involved in hydrogen bonding are represented by transparent surfaces, while the active sites (with bound phosphate) are shown as spheres. Sugar groups are shown as sticks. The C-terminal ends of the silver and cyan subunits, belonging to separate trimers, traverse the interface region in the solvent-filled channels and are shown with their terminal Ser589 (stick) residues poised above the bound phosphate groups.

Volume 1| Part 2| February 2014| Pages 101-109
ISSN: 2052-2525