Walker motifs

{{Short description|ATP-binding protein sequence motifs}} {{Use dmy dates|date=January 2024}} {{Infobox protein family |InterPro=IPR027417 |Name=P-loop containing nucleoside triphosphate hydrolase |CATH= |SCOP= }} 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.<ref name="pmid6329717">{{cite journal | vauthors = Walker JE, Saraste M, Runswick MJ, Gay NJ | title = 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 | journal = The EMBO Journal | volume = 1 | issue = 8 | pages = 945–951 | year = 1982 | pmid = 6329717 | pmc = 553140 | doi = 10.1002/j.1460-2075.1982.tb01276.x }}</ref>

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:<ref name="pmid11916378">{{cite journal | vauthors = Leipe DD, Wolf YI, Koonin EV, Aravind L | title = Classification and evolution of P-loop GTPases and related ATPases | journal = Journal of Molecular Biology | volume = 317 | issue = 1 | pages = 41–72 | date = March 2002 | pmid = 11916378 | doi = 10.1006/jmbi.2001.5378 | url = https://zenodo.org/record/1229904 | name-list-style = amp }}</ref><ref name="isbn0-7167-4684-0">{{cite book | vauthors = Stryer L, Berg JM, Tymoczko JL |title=Biochemistry |url=https://archive.org/details/biochemistry200100jere |url-access=registration |publisher=W.H. Freeman |location=San Francisco |year=2002 |isbn=0-7167-4684-0 }}</ref><ref>{{cite journal | vauthors = Ramakrishnan C, Dani VS, Ramasarma T | title = A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins | journal = Protein Engineering | volume = 15 | issue = 10 | pages = 783–798 | date = October 2002 | pmid = 12468712 | doi = 10.1093/protein/15.10.783 | doi-access = free }}</ref><ref name="pmid2126155">{{cite journal | vauthors = Saraste M, Sibbald PR, Wittinghofer A | title = The P-loop--a common motif in ATP- and GTP-binding proteins | journal = Trends in Biochemical Sciences | volume = 15 | issue = 11 | pages = 430–434 | date = November 1990 | pmid = 2126155 | doi = 10.1016/0968-0004(90)90281-f }}</ref> * RecA and rotor ATP synthase / ATPases (α and β subunits). * Nucleic acid-dependent ATPases: helicases, Swi2, and PhoH ({{InterPro|IPR003714}}) * AAA proteins * STAND NTPases including MJ, PH, AP, and NACHT ATPases * ABC-PilT ATPases * Nucleotide kinases ({{InterPro|IPR000850}}) * G domain proteins: G-proteins (transducin), myosin.

==Walker A motif==

thumb|right|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<sup>2+</sup> 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.<ref name="pmid16072036">{{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 }}</ref> 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.<ref>{{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 }}</ref>

Apart from the conserved lysine, a feature of the P-loop used in phosphate binding is a compound LRLR nest<ref>{{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 }}</ref> 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<ref>{{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 }}</ref> 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}}

=== 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.<ref name="pmid9705307">{{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 }}</ref>

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

===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.<ref name="pmid16412422">{{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 }}</ref>

==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.<ref name="pmid6329717" /> This motif was changed to be hhhhDE, where E denotes a glutamate residue.<ref name="pmid16072036"/> 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.<ref name="pmid16072036"/> 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.<ref name="pmid8332451">{{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 }}</ref>

== 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.<ref>{{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 | article-number = e64415 | date = December 2020 | pmid = 33295875 | pmc = 7758060 | doi = 10.7554/eLife.64415 | veditors = Deane CM, Boudker O | doi-access = free }}</ref>

== References ==

== External links == * [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]

{{DEFAULTSORT:Walker Motifs}} Category:Protein structural motifs