Walker motifs#Walker A motif

Image:Ras-P-loop.png

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.{{cite journal | vauthors = Hanson PI, Whiteheart SW | title = AAA+ proteins: have engine, will work | journal = Nature Reviews. Molecular Cell Biology | volume = 6 | issue = 7 | pages = 519–529 | date = July 2005 | pmid = 16072036 | doi = 10.1038/nrm1684 | s2cid = 27830342 }} 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.{{cite journal | vauthors = Bugreev DV, Mazin AV | title = Ca2+ activates human homologous recombination protein Rad51 by modulating its ATPase activity | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 27 | pages = 9988–9993 | date = July 2004 | pmid = 15226506 | pmc = 454202 | doi = 10.1073/pnas.0402105101 | doi-access = free | bibcode = 2004PNAS..101.9988B }}

Apart from the conserved lysine, a feature of the P-loop used in phosphate binding is a compound LRLR nest{{cite journal | vauthors = Watson JD, Milner-White EJ | title = 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 = Journal of Molecular Biology | volume = 315 | issue = 2 | pages = 171–182 | date = January 2002 | pmid = 11779237 | doi = 10.1006/jmbi.2001.5227 }} 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{{cite journal | vauthors = Bianchi A, Giorgi C, Ruzza P, Toniolo C, Milner-White EJ | title = A synthetic hexapeptide designed to resemble a proteinaceous P-loop nest is shown to bind inorganic phosphate | journal = Proteins | volume = 80 | issue = 5 | pages = 1418–1424 | date = May 2012 | pmid = 22275093 | doi = 10.1002/prot.24038 | s2cid = 5401588 }} 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|date=May 2017}}

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.{{cite journal | vauthors = Zhang M, Stauffacher CV, Lin D, Van Etten RL | title = Crystal structure of a human low molecular weight phosphotyrosyl phosphatase. Implications for substrate specificity | journal = The Journal of Biological Chemistry | volume = 273 | issue = 34 | pages = 21714–21720 | date = August 1998 | pmid = 9705307 | doi = 10.1074/jbc.273.34.21714 | doi-access = free }}

Pyridoxal phosphate (PLP) utilizing enzymes such as cysteine synthase have also been said to resemble a P-loop.{{citation needed|date=April 2024}}

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.{{cite journal | vauthors = Ambudkar SV, Kim IW, Xia D, Sauna ZE | title = The A-loop, a novel conserved aromatic acid subdomain upstream of the Walker A motif in ABC transporters, is critical for ATP binding | journal = FEBS Letters | volume = 580 | issue = 4 | pages = 1049–1055 | date = February 2006 | pmid = 16412422 | doi = 10.1016/j.febslet.2005.12.051 | doi-access = free }}

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. This motif was changed to be hhhhDE, where E denotes a glutamate residue. 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.

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.{{cite journal | vauthors = Koonin EV | title = 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 | journal = Nucleic Acids Research | volume = 21 | issue = 11 | pages = 2541–2547 | date = June 1993 | pmid = 8332451 | pmc = 309579 | doi = 10.1093/nar/21.11.2541 }}

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.{{cite journal | vauthors = Longo LM, Jabłońska J, Vyas P, Kanade M, Kolodny R, Ben-Tal N, Tawfik DS | title = On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment | journal = eLife | volume = 9 | pages = e64415 | date = December 2020 | pmid = 33295875 | pmc = 7758060 | doi = 10.7554/eLife.64415 | veditors = Deane CM, Boudker O | doi-access = free }}

• Activation loop
• Autophosphorylation
• Ca²⁺/calmodulin-dependent protein kinase
• Cell signaling
• Cyclin-dependent kinase
• G protein-coupled receptor
• Nucleoside-diphosphate kinase
• Phosphatase
• Phosphatidylinositol phosphate kinases
• Phospholipid
• Phosphoprotein
• Phosphorylation
• Phosphotransferase
• Signal transduction
• Thymidine kinase
• Thymidine kinase in clinical chemistry
• Thymidylate kinase
• Wall-associated kinase

{{reflist}}

• [http://expasy.org/cgi-bin/get-prodoc-entry?PDOC00017 Prosite entry for Walker A motif, PS00017]
• [http://expasy.org/prosite/PDOC51195 Prosite entry for DEAD box motif PS51195]

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Category:Protein structural motifs