Walker motifs

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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.[1]

Walker A motif[edit]

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 Mg2+ 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 (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.[2] 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.[3]

Apart from the conserved lysine, a feature of the P-loop used in phosphate binding is a compound LRLR nest[4] comprising the four residues xxGK, as above, whose main chain atoms form a phosphate-sized concavity with the NH groups pointing inwards. The hexapeptide SGAGKT has been shown[5] 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.

The Walker A motif is best known for its presence in ATP- and GTP-binding proteins, and is also found in a variety of proteins with phosphorylated substrates. These include ATP synthase (α and β subunits), myosin, transducin, helicases, kinases, AAA proteins, G-proteins, RecA, protein tyrosine phosphatases (see below) and pyridoxal phosphate utilizing enzymes such as cysteine synthase.[6][7][8]

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]

PTPs (protein tyrosine phosphatases) that catalyse the hydrolysis of an inorganic phosphate from a phosphotyrosine residue (the reverse of a tyrosine kinase reaction) contains 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.[9]

A-loop[edit]

The A-loop (Aromatic residue interacting with the adenine ring of ATP) refers to conserved aromatic amino acids, essential for ATP-binding, found about 25 amino acids upstream of the Walker A motif in a subset of P-loop proteins.[10]

Walker B motif[edit]

Walker B motif is a motif in most P-loop proteins situated well downstream of the A-motif. Walker et al reported the consensus sequence of this motif to be [RK]-x(4)-G-x(4)-LhhhhD, 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] The consensus sequence of this motif was more recently reported by Hanson and Whiteheart (2005) to be hhhhDE, where E denotes a glutamate residue.[2] 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.[2] 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.[11]

See also[edit]

References[edit]

  1. ^ a b 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". EMBO J. 1 (8): 945–51. PMC 553140Freely accessible. PMID 6329717. 
  2. ^ a b c Hanson PI, Whiteheart SW (July 2005). "AAA+ proteins: have engine, will work". Nat. Rev. Mol. Cell Biol. 6 (7): 519–29. PMID 16072036. doi:10.1038/nrm1684. 
  3. ^ Bugreev, D. V.; Mazin, A. V. (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: 9988–9993. doi:10.1073/pnas.0402105101. 
  4. ^ Watson, JD; Milner-White EJ (2002). "A novel main-chain anion binding site in proteins: the nest. A particular combination of phi,psi values for successive residues gives rise to anion binding sites that occur commonly and are found at functionally important regions.". Journal of Molecular Biology. 315: 171–182. PMID 11779237. doi:10.1006/jmbi.2001.5227. 
  5. ^ Bianchi, A; Giorgi C; Ruzza P; Toniolo C; Milner-White EJ (2012). "A synthetic peptide designed to resemble a proteinaceous P-loop nest is shown to bind inorganic phosphate.". Proteins. 80: 1418–1424. PMID 22275093. doi:10.1002/prot.24038. 
  6. ^ Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2002). Biochemistry. San Francisco: W.H. Freeman. ISBN 0-7167-4684-0. 
  7. ^ 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. PMID 12468712. doi:10.1093/protein/15.10.783. Retrieved 16 October 2013. 
  8. ^ Saraste M, Sibbald PR, Wittinghofer A (November 1990). "The P-loop--a common motif in ATP- and GTP-binding proteins". Trends Biochem. Sci. 15 (11): 430–4. PMID 2126155. doi:10.1016/0968-0004(90)90281-f. 
  9. ^ 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". J. Biol. Chem. 273 (34): 21714–20. PMID 9705307. doi:10.1074/jbc.273.34.21714. 
  10. ^ 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 Lett. 580 (4): 1049–55. PMID 16412422. doi:10.1016/j.febslet.2005.12.051. 
  11. ^ 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 Res. 21 (11): 2541–7. PMC 309579Freely accessible. PMID 8332451. doi:10.1093/nar/21.11.2541. 

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