ATP-Binding Motif 

The ATP-binding motif, also called the Walker motif, is a structural protein motif that is frequently found in proteins that bind ATP or GTP. It can usually be identified from just the primary structure of a protein using a fingerprint sequence that characterizes proteins as ATP or GTP-binding. Walker et al. (1) identified two regions of sequence conservation: the A region has a stretch of small hydrophobic residues followed by [Gly/Ala] X X Gly X Gly Lys Thr/Ser, where X is any residue. The second region of sequence conservation also has a stretch of small hydrophobic residues, this time ending in a conserved aspartate residue. In the  three-dimensional structures of proteins having the ATP-binding motif, such as adenylate kinase, the hydrophobic residues of the A-region form a buried b-strand, and the glycine-rich region forms a loop, called the P-loop, that interacts with the phosphate of the bound nucleotide. The second conserved region codes for another hydrophobic b-strand, and the conserved aspartate is required for binding the magnesium ion that usually accompanies nucleotides bound to proteins.

 The ATP-binding motif represents a common, but not the only, mode of interaction between proteins and ATP/GTP. For example, it is structurally distinct from the actin fold of proteins such as actin, hsp70, and hexokinase, which bind and hydrolyze ATP or GTP and where a conformational change is implicated in nucleotide binding (2).

References

1. J. E. Walker, M. Saraste, M. Runswick, and N. Gay (1982) EMBO J. 1, 945–951. 

2. W. Kabsch and K. C. Holmes (1995) FASEB J. 9, 167–174.