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. 2006 Oct 6;189(4):1254–1265. doi: 10.1128/JB.01216-06

FIG.4.

FIG.4.

Structure of AgDI. (A and B) Ribbon representations of the monomer of E. faecalis AgDI (A) and of the catalytic domain of Mycoplasma arginini ADI (PDB entry 1S9R without residues 75 to 148, which are not a part of the catalytic domain) (B), both containing the covalently bound substrate in space-filling representation. α helices, β sheets, and loops are colored red, yellow, and green, respectively. (C) Stereo view of the active site of AgDI, showing the density map of 2Fobs − Fcalc, contoured at the 0.9 σ level, around the covalent adduct. The substrate is colored yellow, and the surrounding protein residues are colored gray. O, N, and S atoms are colored red, blue, and green, respectively. (D) Interatomic distances (in angstroms) between the catalytic protein residues and the substrate around the reactive carbon center. The interactions with a fixed water molecule (W1) believed to be important in the mechanism are also represented. The density map of 2Fobs − Fcalc, contoured at 0.75 σ for the covalent amidino complex, is shown. (E) Correspondence between amino acid sequence and secondary structure. Bars, arrows, and lines above the structure denote, respectively, α helices, β strands, and loops (only long loops are depicted), numbered in ascending order from N to C terminus and, when belonging to a repeat, in parentheses and having a subscript that denotes the repeat number. Open triangles under the sequence denote residues having decreased accessibility upon the binding of agmatine. Circles denote decreased accessibility upon dimer (open) and tetramer (shaded) formation. The gray sequence backgrounds highlight residues that are invariant in the AgDIs of E. faecalis, Streptococcus mutans, Pseudomonas aeruginosa, and Arabidopsis thaliana (SwissProt accession numbers Q837U5, Q8DW17, Q9I6J9, and Q8GWW7, respectively). (F) Ribbon diagram of AgDI dimer viewed perpendicularly to the molecular twofold axis. Coloring and substrate representation are as in panel A. (G) Ribbon representation of the AgDI tetramer viewed along one of the three twofold molecular axes. The two subunits of the two dimers (as defined in the text) are shown in different shades of red or blue. The covalently bound substrate is shown in space-filling representation.