P-loop

The Walker A and Walker B motifs are protein sequence motifs, now known to have highly conserved three-dimensional structures. These were first reported in ATP-binding proteins by Walker and co-workers in 1982.

Walker A motif, also known as the Walker loop or P-loop (phosphate-binding loop) is a motif in proteins that is associated with phosphate binding. The motif has the pattern G-x(4)-GK-[TS], where G, K, T and S denote glycine, lysine, threonine and serine residues respectively, and x denotes any amino acid. It is present in many ATP or GTP utilizing proteins; it is the β phosphate of the nucleotide that is bound. The lysine (K) residue in the Walker A motif, together with the main chain NH atoms, are crucial for nucleotide-binding. It is a glycine-rich loop preceded by a beta strand and followed by an alpha helix; these features are typically part of an α/β domain with four strands sandwiched between two helices on each side. The phosphate groups of the nucleotide are also coordinated to a divalent cation such as a magnesium, calcium, or manganese(II) ion.

Apart from the conserved lysine, a feature of the P-loop used in phosphate binding is a compound LRLR nest comprising the four residues xxGK, as above, whose mainchain atoms form a phosphate-sized concavity with the NH groups pointing inwards. The hexapeptide SGAGKT has been shown to bind inorganic phosphate strongly; since such a short peptide does not form an alpha helix, this suggests that it is the nest, rather than being at the N-terminus of a helix, that is the main phosphate binding feature.

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