Walker motifs

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P-loop containing nucleoside triphosphate hydrolase
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InterPro IPR027417

The Walker A and Walker B motifs are protein sequence motifs, known to have highly conserved three-dimensional structures. These were first reported in ATP-binding proteins by Walker and co-workers in 1982. [1]

Contents

Of the two motifs, the A motif is the main "P-loop" responsible for binding phosphate, while the B motif is a much less conserved downstream region. The P-loop is best known for its presence in ATP- and GTP-binding proteins, and is also found in a variety of proteins with phosphorylated substrates. Major lineages include: [2] [3] [4] [5]

Walker A motif

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 ion as green sphere and the side chains of the amino acids K16 and S17 are shown as sticks. Ras-P-loop.png
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 ion as green sphere and the side chains of the amino acids K16 and S17 are shown as sticks.

Walker A motif, also known as the Walker loop, or P-loop, or 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. [6] 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. [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. The synthetic hexapeptide SGAGKT has been shown [9] 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.

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.[ citation needed ]

Similar folds

PTPs (protein tyrosine phosphatases) that catalyse the hydrolysis of an inorganic phosphate from a phosphotyrosine residue (the reverse of a tyrosine kinase reaction) contain a motif which folds into a P-loop-like structure with an arginine in the place of the conserved lysine. The conserved sequence of this motif is C-x(5)-R-[ST], where C and R denote cysteine and arginine residues respectively. [10]

Pyridoxal phosphate (PLP) utilizing enzymes such as cysteine synthase have also been said to resemble a P-loop.[ citation needed ]

A-loop

The A-loop (aromatic residue interacting with the adenine ring of ATP) refers to conserved aromatic amino acids, essential for ATP-binding, found in about 25 amino acids upstream of the Walker A motif in a subset of P-loop proteins. [11]

Walker B motif

Walker B motif is a motif in most P-loop proteins situated well downstream of the A-motif. The consensus sequence of this motif was reported to be [RK]-x(3)-G-x(3)-LhhhD, where R, K, G, L and D denote arginine, lysine, glycine, leucine and aspartic acid residues respectively, x represents any of the 20 standard amino acids and h denotes a hydrophobic amino acid. [1] This motif was changed to be hhhhDE, where E denotes a glutamate residue. [6] The aspartate and glutamate also form a part of the DEAD/DEAH motifs found in helicases. The aspartate residue co-ordinates magnesium ions, and the glutamate is essential for ATP hydrolysis. [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. [12]

Evolutionary connections

There is a hypothesis that the Walker A phosphate binding motif can be evolutionarily related to Rossman's fold phosphate binding motif because of the shared principles in the location of the binding loop between the first β-strand and α-helix in the αβα sandwich fold and positioning of the functionally important aspartate on the tip of the second β-strand. [13]

See also

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References

  1. 1 2 Walker JE, Saraste M, Runswick MJ, 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". The EMBO Journal. 1 (8): 945–951. doi:10.1002/j.1460-2075.1982.tb01276.x. PMC   553140 . PMID   6329717.
  2. ↑ Leipe DD, Wolf YI, Koonin EV, Aravind L (March 2002). "Classification and evolution of P-loop GTPases and related ATPases". Journal of Molecular Biology. 317 (1): 41–72. doi:10.1006/jmbi.2001.5378. PMID   11916378.
  3. ↑ Stryer L, Berg JM, Tymoczko JL (2002). Biochemistry . San Francisco: W.H. Freeman. ISBN   0-7167-4684-0.
  4. ↑ Ramakrishnan C, Dani VS, Ramasarma T (October 2002). "A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins". Protein Engineering. 15 (10): 783–798. doi: 10.1093/protein/15.10.783 . PMID   12468712.
  5. ↑ Saraste M, Sibbald PR, Wittinghofer A (November 1990). "The P-loop--a common motif in ATP- and GTP-binding proteins". Trends in Biochemical Sciences. 15 (11): 430–434. doi:10.1016/0968-0004(90)90281-f. PMID   2126155.
  6. 1 2 3 Hanson PI, Whiteheart SW (July 2005). "AAA+ proteins: have engine, will work". Nature Reviews. Molecular Cell Biology. 6 (7): 519–529. doi:10.1038/nrm1684. PMID   16072036. S2CID   27830342.
  7. ↑ Bugreev DV, Mazin AV (July 2004). "Ca2+ activates human homologous recombination protein Rad51 by modulating its ATPase activity". Proceedings of the National Academy of Sciences of the United States of America. 101 (27): 9988–9993. Bibcode:2004PNAS..101.9988B. doi: 10.1073/pnas.0402105101 . PMC   454202 . PMID   15226506.
  8. ↑ Watson JD, Milner-White EJ (January 2002). "A novel main-chain anion-binding site in proteins: the nest. A particular combination of phi,psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions". Journal of Molecular Biology. 315 (2): 171–182. doi:10.1006/jmbi.2001.5227. PMID   11779237.
  9. ↑ Bianchi A, Giorgi C, Ruzza P, Toniolo C, Milner-White EJ (May 2012). "A synthetic hexapeptide designed to resemble a proteinaceous P-loop nest is shown to bind inorganic phosphate". Proteins. 80 (5): 1418–1424. doi:10.1002/prot.24038. PMID   22275093. S2CID   5401588.
  10. ↑ Zhang M, Stauffacher CV, Lin D, Van Etten RL (August 1998). "Crystal structure of a human low molecular weight phosphotyrosyl phosphatase. Implications for substrate specificity". The Journal of Biological Chemistry. 273 (34): 21714–21720. doi: 10.1074/jbc.273.34.21714 . PMID   9705307.
  11. ↑ Ambudkar SV, Kim IW, Xia D, Sauna ZE (February 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 (4): 1049–1055. doi: 10.1016/j.febslet.2005.12.051 . PMID   16412422.
  12. ↑ Koonin EV (June 1993). "A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication". Nucleic Acids Research. 21 (11): 2541–2547. doi:10.1093/nar/21.11.2541. PMC   309579 . PMID   8332451.
  13. ↑ Longo LM, Jabłońska J, Vyas P, Kanade M, Kolodny R, Ben-Tal N, Tawfik DS (December 2020). Deane CM, Boudker O (eds.). "On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment". eLife. 9: e64415. doi: 10.7554/eLife.64415 . PMC   7758060 . PMID   33295875.
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