Abstract
Nests are common three to six amino acid residue motifs in proteins where successive main chain NH groups bind anionic atoms or groups. On average 8% of residues in proteins belong to nests. Nests form a key part of a number of phosphate binding sites, notably the P-loop, which is the commonest of the binding sites for the phosphates of ATP and GTP. They also occur regularly in sites that bind [Fe2S2](RS)4 [Fe3S4](RS)3 and [Fe4S4](RS)4 iron-sulfur centers, which are also anionic groups. Both phosphates and iron-sulfur complexes would have occurred in the precipitates within hydrothermal vents of moderate temperature as key components of the earliest metabolism and it is likely existing organisms emerging in this milieu would have benefited from evolving molecules binding such anions. The nest conformation is favored by high proportions of glycine residues and there is evidence for glycine being the commonest amino acid during the stage of evolution when proteins were evolving so it is likely nests would have been common features in peptides occupying the membranes at the dawn of life.
Article PDF
Similar content being viewed by others
Abbreviations
- ϕ, ψ::
-
For amino acid i, phi (ϕ) is the dihedral angle between the Ci−1-Ni-Cαi-Ci atoms and psi (ψ) is the dihedral angle between the Ni-Cαi-Ci-Ni+1 atoms (i-1 and i+1 are the preceding and succeeding residues).
References
Allen, J. F.: 1993, Redox Control of Transcription: Sensors, Response Regulators, Activators and Repressors, FEBS Letters 332 203–207.
Baltscheffsky, M., Schultz, A. and Baltscheffsky, H.: 1999, H +-PPases: A Tightly Membrane-Bound Family, FEBS Letters 457 527–533.
Baltscheffsky, M., von Stedingk, L-V., Heldt, H-W. and Klingenberg, M.: 1966, Inorganic Pyrophos-phate; Formation in Bacterial Photophosphorylation, Science 153 1120–1122.
Baymann, F., Lebrun, E., Brugna, M., Schoepp-Cothenet, B., Giudici-Orticoni, M.T., and Nitschke, W.: 2003, The Redox Construction Kit: Pre-LUCA evolution of energy-conserving enzymes, Phil. Trans. R. Soc.London. B358, 267–274.
Beinert, H., Holm, R. H. and Munck, E.: 1997, Iron-Sulfur Clusters: NatureÕs Modular Multipurpose Structures, Science 277 653–659.
Bonomi, F., Werth, M. T. and Kurtz, D. M.: 1985, Assembly of Fe S (SR)2−(n=2,4) in Aqueous Me-dia from Iron Salts, Thiols and Sulfur, Sulfide, Thiosulfide Plus Rhodonase, Inorganic Chemistry 24 4331–4335.
Cammack, R.: 1996, Iron and Sulfur in the Origin and Evolution of Biological Energy Conservation Systems, in H. Baltscheffsky (ed.), Origin and Evolution of Biological Energy Systems,VCH Publishers, Deerfield Beach, Florida, pp. 43–69.
Chen, K., Hirst, J., Camba, R., Bonagura, C. A., Stout, C. D., Burgess, B. K. and Armstrong, F. A.: 2000, Atomically Defined Mechanism for Proton Transfer to a Buried Redox Centre in a Protein, Nature405, 814–817.
Dreusicke, D. and Schulz, G. E.: 1986, The Glycine-Rich Loop of Adenylate Kinase Forms a Giant Anion Hole, FEBS Letters 208 301–304.
Eck, R. V. and Dayhoff, M. O.: 1966, Evolution of the Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences, Science 152 363–366.
Filtness, M. J., Butler, I. B. and Rickard, D.: 2003, The Origin of Life: The Properties of Iron Sulphide Membranes, Applied Earth Science (Trans. Inst. Min. Metall.) 112B, 171–172.
Flint, D. H. and Allen, R. A.: 1996, Iron-Sulfur Proteins with Non-Redox Functions, Chem. Rev. 96 2315–2334.
Fox, S. W.: 1959, Biological Overtones of the Thermal Theory of Biochemical Origins, AIBS Bulletin, January Edition, 20–23.
Fujii, T., Hata,Y., Wakagi, T., Tanaka, N. and Oshima. T.: 1996, Novel Zinc-Binding Center in Thermoacidophilic Archeal Ferredoxins, Nature Struct. Biol. 3, 834.
Hall, D. O., Cammack, R. and Rao, K. K.: 1971, Role for Ferredoxins in the Origin of Life and Biological Evolution, Nature233, 136–138.
Heinen, W. and Lauwers, A. M.: 1996, Organic Sulfur Compounds Resulting from the Interaction of Iron Sulfide, Hydrogen Sulfide and Carbon Dioxide in an Anaerobic Aqueous Environment, Origins Life Evol. Biosph. 26 131–150.
Hennet, R. J-C., Holm, N. G. and Engel, M. H.: 1992, Abiotic Synthesis of Amino Acids under Hydrothermal Conditions and the Origin of Life: A Perpetual Phenomenon? Naturwissenschaften 79, 361–365.
Johnson, M. K.: 1996, Iron-Sulfur Proteins, in B. B. King (ed.), Encyclopedia of Inorganic Chemistry, Vol. 4, Wiley, Chichester, pp. 1896–1915.
Kaschke, M., Russell, M. J. and Cole, W. J.: 1994, [FeS/FeS 2]. A Redox System for the Origin of Life, Origins Life Evol. Biosphere 24 43–56.
Marshall, W. L.: 1994, Hydrothermal Synthesis of Amino Acids, Geochim. Cosmochim. Acta 58 2099–2106.
Martin, W. and Russell, M. J.: 2003, On the Origin of Cells: An Hypothesis for the Evolutionary Transitions from Abiotic Geochemistry to Chemoautorophic Prokaryotes, and from Prokaryotes to Nucleated Cells, Phil. Trans. R. Soc. London. B358, 27–85.
Pai, E. F., Krengel, U., Petsko, G. A., Goody, R. S., Kabsch, W. and Wittinghofer, A.: 1990, Refined Crystal Structure of the Triphosphate Conformation of H-ras p21, EMBO J. 9 2351–2359.
Pal, D., Weiss, M. and Suehnel, J.: 2002, New Principles of Protein Structure: Nests, Eggs and Then What? Angewandte Chemie 41 4663–4665.
Ramakrishnan, C., Dani, V. S. and Ramasarma, T.: 2002, A Conformational Analysis of Walker Motif: A Nucleotide Binding and Other Proteins, Prot. Eng. 15 783–798.
Rees, D. C. and Howard, J. B.: 2003, The Interface between the Biological and Inorganic Worlds: Iron-Sulfur Metalloclusters, Science 300 929–931.
Russell, M. J. and Hall, A. J.: 1997, The Emergence of Life from Iron Monosulphide Bubbles at a Submarine Hydrothermal Redox and pH Front, J. Geol. Soc. London 154 377–402.
Russell, M. J., Hall, A. J. and Mellersh, A. R.: 2003, On the Dissipation of Thermal and Chem-ical Energies on the Early Earth: The Onsets of Hydrothermal Convection, Chemiosmosis, Genetically Regulated Metabolism and Oxygenic Photosynthesis, in R. Ikan (ed.), Natural and Laboratory-Simulated Thermal Geochemical Processes, Kluwer Academic Publishers, Dordrecht, pp. 325–388.
Russell, M. J., Daniel, R. M., Hall, A .J. and Sherringham, J.: 1994, A Hydrothermally Precipitated Catalytic Iron Sulphide Membrane as a First Step Toward Life, J. Mol. Evol. 39 231–243.
Steigerwald, V. J., Beckler, G. S. and Reeve, J. N.: 1990, Conservation of Hydrogenase and Poly-ferredoxin Structures in the Hyperthermophilic Archaebacterium Methanothermus fervidus, J. Bact. 172 4715–4718.
Sticht, H. and Rosch, P.: 1998, The Structure of Iron-Sulfur Proteins, Prog. Biophys. Mol. Biol. 70 95–136.
Trifonov, E. N., Kirzhner, A., Kirzhner, V. M. and Berezhovsky, I. N.: 2001, Distinct Stages of Protein Evolution as Suggested by Protein Sequence Analysis, J. Mol. Evol. 53 394–401.
Vaughan, D. J. and Craig, J. R.: 1978, Mineral Chemistry of Natural Sulfides, Cambridge University Press, Cambridge, p. 493.
Via, A., Ferre, F., Brannetti, B., Valencia, A. and Hemer-Citterich, M.: 2000, Three-Dimensional View of the Surface Motif Associated with the P-Loop Structure, J. Mol. Biol. 303 45–465.
Vitagliano, L., Masullo, M., Sica, F., Zagari, A, and Bocchini, V.: 2001, Crystal Structure of S. Sulfataricus EF-1α in Complex with GDP Reveals Novel Features in Nucleotide Binding and Exchange, EMBO J. 20 5305–5311.
Watson, J. D. and Milner-White, E. J.: 2002a, A Novel Main Chain Anion Binding Site in Proteins: The Nest. A Particular Combination of ϕsψ Angles in Successive Residues Gives Rise to Anion-Binding Sites that Occur Commonly and Are Found Often at Functionally Important Regions, J. Mol. Biol. 315 199–207.
Watson, J. D. and Milner-White, E. J.: 2002b, The Conformations of Polypeptide Chains where the ϕsψ Values of Alternating Residues are Enantiomeric. Their Occurrence in Cation and Anion Binding Regions of Proteins, J. Mol. Biol. 315 187–198.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Milner-White, E.J., Russell, M.J. Sites for Phosphates and Iron-Sulfur Thiolates in the First Membranes: 3 to 6 Residue Anion-Binding Motifs (Nests). Orig Life Evol Biosph 35, 19–27 (2005). https://doi.org/10.1007/s11084-005-4582-7
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s11084-005-4582-7