Methionyl-tRNA synthetase zinc binding domain. Three-dimensional structure and homology with rubredoxin and gag retroviral proteins.
Methionyl-tRNA synthetase from Escherichia coli contains one tightly bound zinc atom per subunit. The region encompassing residues 138 to 163 of this enzyme is responsible for the metal binding. A 28-mer peptide corresponding to these residues was expressed in vivo and shown to contain approximately 1 mol of tightly bound Zn/mol of peptide. In this study, the three-dimensional solution structure of this peptide was solved by means of two-dimensional proton NMR spectroscopy. A total of 133 nuclear Overhauser effect distance constraints and 22 dihedral angle restraints were used for the calculations, using a hybrid distance-geometry-simulated annealing strategy. Excluding the first four residues, the resulting structure is well-defined (r.m.s.d. 0.71 A for backbone atoms) and composed of a series of four tight turns. The second and the fourth turns are composed of CXXC sequences which are structurally homologous to the NH-S turns found in the metal binding sites of gag retroviral proteins and rubredoxin. The solution structure of the zinc binding peptide shows significant discrepancies with the crystal structure of methionyl-tRNA synthetase.
Fourmy
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Laboratoire de Biochimie, URA 240 CNRS Ecole Polytechnique, Palaiseau, France.
Dardel
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Blanquet
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D000595:Amino Acid Sequence; D003545:Cysteine; D004926:Escherichia coli / Q000201:enzymology; D015683:Gene Products, gag / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008718:Methionine-tRNA Ligase / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D010446:Peptide Fragments / Q000737:chemistry; D011487:Protein Conformation; D011498:Protein Precursors / Q000737:chemistry; D012416:Rubredoxins / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D015032:Zinc / Q000378:metabolism*
D015683:Gene Products, gag; D010446:Peptide Fragments; D011498:Protein Precursors; D012416:Rubredoxins; C059767:p55 gag precursor protein, Human immunodeficiency virus 1; D008718:Methionine-tRNA Ligase; D015032:Zinc; D003545:Cysteine