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Figure 2
Defining features of KCX sites. (a) Examples of proteins requiring functional carboxylated lysine residues. Examples of Kcx as a co-catalytic determinant involved in the formation of binuclear and mononuclear metal-ion centers (e.g. urease and RuBisCo, respectively) and Kcx as a catalytic determinant (e.g. class D β-lactamase). (b) Dispersion along protein sequences of amino acids that are part of the KCX site. Gray bars represent protein sequences, which are scaled for comparison. Cyan portions represent the fragment from the first to the last of the amino acids found in KCX sites. Yellow dots represent amino acids that are part of the KCX site and the red dot represents the Kcx residue (only 1ejx, 3kdn and 3isg shown). The left axis shows the PDB code (PDB ID) and the right axis the percentage of the extent of the protein sequences that the KCX sites occupy. A lack of a sequence motif was concluded (see Supplementary Fig. S1) (c) Summary of metal-ion center motifs. The side chains of the residues interacting with the metal ion are given in parentheses. For example, (H,H,D)Zn represents the side chains of two His residues and one Asp residue interacting with a zinc ion. Kcx side chains can either interact with one ion, e.g. (H,H,D)Zn· · ·KCX, or can bridge two metal ions, e.g. (H,H,D)Zn· · ·KCX· · ·Zn(H,H). The stick representation shows detail of the metal-ion centers of urease and RuBisCo.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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