Figure 5

Mapping of high propensity fragments for PDB entry 1woh [30], shown on a backdrop of the multiple alignment of ureohydrolase superfamily enzymes. The start positions of high propensity fragments are marked by triangles in the last six rows of each panel. Binned propensity values are given in the color legend. Prop8, propensities derived from FL8, GO level 3 mapped from GO:0016813; Prop8_1, propensities derived from FL8, GO level 4 mapped from GO:0016813; Prop8_2, propensities derived from FL8, GO level 4 mapped from GO: GO:0046872; Prop16, Prop16_1, and Prop16_2 refer to the same information, except that it was derived from FL16. The residue numbers are indicated for 1woh, which is DR agmatinase: Agm_Dra (SWISS-PROT entry Q9RZ04). Other proteins in the alignment are Agm_Eco for agmatinase from E. coli (P60651); Agm_hum for agmatinase from human mitochondria (Q9BSE5, residues 1-35 deleted); Arg_rat for arginase I from rat liver (P07824); Arg_Bca for arginase from Bacillus caldovelox (P53608); and PAH_Scl for proclavaminate amidinohydrolase from Streptomyces clavuligerus (P37819). Secondary structure elements are shown as cylinders for helices and fat arrows for β-strands. Strictly conserved residues and semi-conserved residues are colored red and yellow, respectively. Above the sequences, blue circles indicate the residues that coordinate Mn²⁺ ions. In the same panel as residue numbers, brick-red colored inverted triangles indicate residues putatively interacting with the guanidinium group of agmatine. Green inverted triangles indicate the residues observed in the crystal structure to be interacting with the bound inhibitor. Further details may be obtained from [30]. The figure was drawn using the program ALSCRIPT [69].