ATP‐binding Motifs


Adenosine 5′‐triphosphate (ATP) binds to a great number of proteins to elicit a wide variety of effects, including energy production and molecular signalling. Proteins have evolved different strategies to specifically recognize ATP, utilizing different ways of binding the phosphoryl moieties as well as the adenine base. The most common, conserved sequence and structural motif for binding ATP is the Walker‐A motif, or P‐loop, found in many different protein structural families. Greater variation in the sequence of the P‐loop is being recognized, as more ATP‐binding proteins are being structurally and functionally characterized. In contrast to the P‐loop, recognition of the adenine base often makes use of conserved structural motifs of main‐chain atoms via hydrogen‐bonding interactions, or side‐chains in stacking interactions, without a definitive amino acid sequence pattern.

Key concepts:

  • A major class of ATP‐binding proteins are those that contain a P‐loop or Walker‐A motif.

  • P‐loops or glycine‐rich loops function by binding the phosphoryl groups of ATP.

  • Several sequence variations on the Walker‐A motif are now known and have been functionally characterized.

  • The Walker‐B motif contains a conserved acidic residue (Glu/Asp) that functions to bind directly or indirectly a metal ion important in catalysis.

  • Adenine‐binding does not occur through specific sequence motifs, but rather uses a conserved pattern of polar and nonpolar interactions within a structural motif.

  • Both main‐chain hydrogen bonding and aromatic residue stacking contribute to adenine‐binding by proteins.

Keywords: P‐loop; nucleotide‐binding; protein fold; sequence motif; adenone‐5′‐triphosphate

Figure 1.

Crystal structure of yeast adenylate kinase (pale green) bound to the bi‐substrate inhibitor bis(adenosine)‐5′‐pentaphosphate (Ap5A) and Mg2+ at 1.96 Å resolution (PDB 1AKY). The β‐strand‐loop‐α‐helix motif containing the P‐loop is coloured light blue, with the catalytic Lys16 coloured blue, and the three Gly residues of the P‐loop coloured yellow. Hydrogen‐bonding interactions with the Ap5A inhibitor (red=oxygen, blue=nitrogen, grey=carbon and green=phosphorous) are indicated as grey dashed lines. This figure was prepared using PyMol 1.0r2 (

Figure 2.

Crystal structure of biotin carboxylase (pale green) from Staphylococcus aureus (PDB 2VPQ), highlighting interactions between ATP with proteins belonging to the ATP‐grasp fold. The ATP‐grasp fold consists of a α/β/α unit, including a pair of antiparallel β‐strands connected by a loop. This loop (light blue) contains a conserved Gly (Gly161) that forms a hydrogen bond with the β‐phosphoryl moiety. Additionally, sequence‐conserved hydrogen‐bonding interactions involve a polar residue (Glu199) with the N6 atom of the adenine base, as well as a pair of Lys residues (Lys115, Lys157) with the α‐ and β‐phosphoryl moietieis of ATP. This figure was prepared using PyMol 1.0r2 (



Ambudkar SV, Kim I‐W, Xia D and Sauna ZE (2006) The A‐loop, a novel conserved aromatic acid subdomain upstream of the Walker A motif in ABC transporters, is critical for ATP binding. FEBS Letters 580: 1049–1055.

Aravind L and Koonin EV (1999) DNA polymerase beta‐like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Research 27: 1609–1618.

Barouch‐Bentov R, Che J, Lee CC et al. (2009) A conserved salt bridge in the G loop of multiple protein kinases is important for catalysis and for in vivo Lyn function. Molecular Cell 33: 43–52.

Bártová I, Otyepka M, Kriz Z and Koca J (2004) Activation and inhibition of cyclin‐dependent kinase‐2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine‐rich loop. Protein Science 13: 1449–1457.

Berman HM, Westbrook J, Feng Z et al. (2000) The Protein Data Bank. Nucleic Acids Research 28: 235–242.

Bossemeyer D (1994) The glycine‐rich sequence of protein kinases: a multifunctional element. Trends in Biochemical Sciences 19: 201–205.

Carrier I and Gros P (2008) Investigating the role of the invariant carboxylate residues E552 and E1197 in the catalytic activity of Abcb1a (mouse Mdr3). FEBS Journal 275: 3312–3324.

Cordin O, Tanner NK, Doère M, Linder P and Banroques J (2004) The newly discovered Q motif of DEAD‐box RNA helicases regulates RNA‐binding and helicase activity. EMBO Journal 23: 2478–2487.

Delbaere LTJ, Sudom AM, Prasad L, Leduc Y and Goldie H (2004) Structure/function studies of phosphoryl transfer by phosphoenolpyruvate carboxykinase. Biochimica et Biophysica Acta 1697: 271–278.

Denessiouk KA and Johnson MS (2000) When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Proteins: Structure, Function, and Genetics 38: 310–326.

Denessiouk KA, Rantanen V‐V and Johnson MS (2001) Adenine recognition: a motif present in ATP‐, CoA‐, NAD‐, NADP‐ and FAD‐dependent proteins. Proteins: Structure, Function, and Genetics 44: 282–291.

Finn RD, Tate J, Mistry J et al. (2008) The Pfam protein families database. Nucleic Acids Research 36: D281–D288.

Galperin MY and Koonin EV (1997) A diverse family of enzymes with ATP‐dependent carboxylate‐amine/thiol ligase activity. Protein Science 6: 2639–2643.

Hirai TJ, Tsigelny I and Adams JA (2000) Catalytic assessment of the glycine‐rich loop of the v‐Fps oncoprotein using site‐directed mutagenesis. Biochemistry 39: 13276–13284.

Jeoung J‐H, Giese T, Grunwald M and Dobbek H (2009) CooCl from Carboxydothermus hydrogenformans is a nickel‐binding ATPase. Biochemistry 48: 11505–11513.

Jha S, Karmani N, Lynn AM and Prasad R (2003) Purification and characterization of the N‐terminal nucleotide binding domain of an ABC drug transporter of Candida albicans: uncommon cysteine 193 of Walker A is critical for ATP hydrolysis. Biochemistry 42: 10822–10832.

Kawakami H, Ozaki S, Suzuki S et al. (2006) The exceptionally tight affinity of DnaA for ATP/ADP requires a unique aspartic acid residue in the AAA+ sensor 1 motif. Molecular Microbiology 62: 1310–1324.

Kim I‐W, Peng X‐H, Sauna ZE et al. (2006) The conserved tyrosine residues 401 and 1044 in ATP sites of human P‐glycoprotein are critical for ATP‐binding and hydrolysis: evidence for a conserved subdomain, the A‐loop in the ATP‐binding cassette. Biochemistry 45: 7605–7616.

Kobayashi N and Go N (1997) ATP‐binding proteins with different folds share a common ATP‐binding structural motif. Nature Structural & Molecular Biology 4: 6–7.

Koonin EV (1993) A superfamily of ATPases with diverse functions containing either classical or deviant ATP‐binding motif. Journal of Molecular Biology 229: 1165–1174.

Koonin EV, Wolf YI and Aravind L (2000) Protein fold recognition using sequence profiles and its application in structural genomics. Advances in Protein Chemistry 54: 245–275.

Kuttner YY, Sobolev V, Raskind A and Edelman M (2003) A consensus‐binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine‐containing complexes. Proteins: Structure, Function, and Genetics 52: 400–411.

Leipe DD, Koonin EV and Aravind L (2003) Evolution and classification of P‐loop kinases and related proteins. Journal of Molecular Biology 333: 781–815.

Leipe DD, Koonin EV and Aravind L (2004) STAND: a class of P‐loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. Journal of Molecular Biology 343: 1–28.

Leipe DD, Wolf YI, Koonin EV and Aravind L (2002) Classification and evolution of P‐loop GTPases and related ATPases. Journal of Molecular Biology 317: 41–72.

Mao L, Wang Y, Liu Y and Hu X (2003) Multiple intermolecular interaction modes of positively charged residues with adenine in ATP‐binding proteins. Journal of the American Chemical Society 125: 14216–14217.

Mao L, Wang Y, Liu Y and Hu X (2004) Molecular determinants for ATP‐binding in proteins: a data mining and quantum chemical analysis. Journal of Molecular Biology 336: 787–807.

Milner‐White EJ, Coggins JR and Anton IA (1991) Evidence for an ancestral core structure in nucleotide‐binding proteins with the type A motif. Journal of Molecular Biology 221: 751–754.

Mitchell MS, Matsuzaki S, Imai S and Rao VB (2002) Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases. Nucleic Acids Research 30: 4009–4021.

Moodie SL, Mitchell BO and Thornton JM (1996) Protein recognition of adenylate: an example of a fuzzy recognition template. Journal of Molecular Biology 263: 486–500.

Nagy M, Wu H‐C, Liu Z, Kedzierska‐Mieszkowska S and Zolkiewski M (2009) Walker‐A threonine couples nucleotide occupancy with the chaperone activity of the AAA+ ATPase ClpB. Protein Science 18: 287–293.

Rai V, Gaur M, Kumar A et al. (2008) A novel catalytic mechanism for ATP hydrolysis employed by the N‐terminal nucleotide‐binding domain of Cdr1p, a multidrug ABC transporter of Candida albicans. Biochimica et Biophysica Acta 1778: 2143–2153.

Rai V, Gaur M, Shukla S et al. (2006) Conserved Asp327 of Cdr1p of Candida albicans has acquired a new role in ATP hydrolysis. Biochemistry 45: 14726–14739.

Saraste M, Sibbald PR and Wittinghofer A (1990) The P‐loop – a common motif in ATP‐ and GTP‐binding proteins. Trends in Biochemical Sciences 15: 430–434.

Schulz GE (1992) Binding of nucleotides by proteins. Current Opinion in Structural Biology 2: 61–67.

Schulz GE, Elzinga M, Marx F and Schirmer RH (1974) Three‐dimensional structure of adenylate kinase. Nature 250: 120–123.

Tanner NK, Cordin O, Banroques J, Doere M and Lidner P (2003) The Q‐motif: a newly identified motif in DEAD box helicases may regulate ATP‐binding and hydrolysis. Molecular Cell 11: 127–138.

Tari L, Matte A, Pugazhenthi U, Goldie H and Delbaere LTJ (1996) Snapshot of an enzyme reaction intermediate in the structure of the ATP‐oxalate ternary complex of Escherichia coli PEP carboxykinase. Nature Structural & Molecular Biology 3: 355–363.

Traut TW (1994) The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide binding sites. European Journal of Biochemistry 222: 9–19.

Tsay JM, Slippy J, Feiss M and Smith DE (2009) The Q motif of a viral packaging motor governs its force generation and communicates ATP recognition to DNA interaction. Proceedings of the National Academy of Sciences of the USA 106: 14335–14360.

Walker JE, Saraste M, Runswick M and Gay NJ (1982) Distantly related sequences in the alpha‐ and beta‐subunits of ATP synthase, myosin, kinases and other ATP‐requiring enzymes and a common nucleotide binding fold. EMBO Journal 1: 945–951.

Zheng J, Knighton DR, ten Eyck LF et al. (1993) Crystal structure of the catalytic subunit of cAMP‐dependent protein kinase complexed with MgATP and peptide inhibitor. Biochemistry 32: 2154–2161.

Further Reading

Chakrabarti P and Samanta U (1995) CH/π interaction in the packing of the adenine ring in protein structures. Journal of Molecular Biology 251: 9–14.

Fry DC, Kuby SA and Mildvan AS (1986) ATP‐binding site of adenylate kinase: mechanistic implications of homology with ras‐encoded p21, F1‐ATPase, and other nucleotide‐binding proteins. Proceedings of the National Academy of Sciences of the USA 83: 907–911.

Kjeldgaard M, Nyborg J and Clark BF (1996) The GTP binding motif: variations on a theme. Federation of American Societies for Experimental Biology Journal 10: 1347–1368.

Smith CA and Rayment I (1996) Active site comparisons highlight structural similarities between myosin and other P‐loop proteins. Biophysical Journal 70: 1590–1602.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Matte, Allan, and Delbaere, Louis TJ(Apr 2010) ATP‐binding Motifs. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0003050.pub2]