Walker motifs
ATP-binding protein sequence motifs
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]
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]
- 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
![](http://upload.wikimedia.org/wikipedia/commons/thumb/0/06/Ras-P-loop.png/220px-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. [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.
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]
See also
- Activation loop
- Autophosphorylation
- Ca 2+ /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
References
- 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): 945–51. doi : 10.1002/j.1460-2075.1982.tb01276.x . PMC 553140 . PMID 6329717 .
- ↑ Leipe D.D.; Wolf Y.I.; Koonin E.V. & Aravind, L. (2002). "Classification and evolution of P-loop GTPases and related ATPases" . J. Mol. Biol . 317 (1): 41–72. doi : 10.1006/jmbi.2001.5378 . PMID 11916378 .
- ↑ Stryer L, Berg JM, Tymoczko JL (2002). Biochemistry . San Francisco: W.H. Freeman. ISBN 0-7167-4684-0 .
- ↑ 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): 783–98. doi : 10.1093/protein/15.10.783 . PMID 12468712 . Retrieved 16 October 2013 .
- ↑ 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): 430–4. doi : 10.1016/0968-0004(90)90281-f . PMID 2126155 .
- 1 2 3 Hanson PI, Whiteheart SW (July 2005). "AAA+ proteins: have engine, will work". Nature Reviews. Molecular Cell Biology . 6 (7): 519–29. doi : 10.1038/nrm1684 . PMID 16072036 . S2CID 27830342 .
- ↑ 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): 9988–93. Bibcode : 2004PNAS..101.9988B . doi : 10.1073/pnas.0402105101 . PMC 454202 . PMID 15226506 .
- ↑ 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): 171–82. doi : 10.1006/jmbi.2001.5227 . PMID 11779237 .
- ↑ 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): 1418–24. doi : 10.1002/prot.24038 . PMID 22275093 . S2CID 5401588 .
- ↑ 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): 21714–20. doi : 10.1074/jbc.273.34.21714 . PMID 9705307 .
- ↑ 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): 1049–55. doi : 10.1016/j.febslet.2005.12.051 . PMID 16412422 .
- ↑ 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): 2541–7. doi : 10.1093/nar/21.11.2541 . PMC 309579 . PMID 8332451 .