Walker motifs

The phosphate groups of the nucleotide are also coordinated to a divalent cation such as a magnesium, calcium, or manganese(II) ion.

[7] Apart from the conserved lysine, a feature of the P-loop used in phosphate binding is a compound LRLR nest[8] comprising the four residues xxGK, as above, whose main chain atoms form a phosphate-sized concavity with the NH groups pointing inwards.

Upon nucleotide hydrolysis the loop does not significantly change the protein conformation, but stays bound to the remaining phosphate groups.

Walker motif A-binding has been shown to cause structural changes in the bound nucleotide, along the line of the induced fit model of enzyme binding.

[6] There is considerable variability in the sequence of this motif, with the only invariant features being a negatively charged residue following a stretch of bulky, hydrophobic amino acids.

Alignment of the H-Ras mutant A59G mutants in complex with GppNHp (green cartoon) and GDP (cyan cartoon). The P-loop main chain is shown in red, the Mg 2+ ion as green sphere and the side chains of the amino acids K16 and S17 are shown as sticks.