title: Molecular strategies to replace the structural metal site in the prokaryotic zinc finger domain.
abstract: The specific arrangement of secondary elements in a local motif often totally relies on the formation of coordination bonds between metal ions and protein ligands. This is typified by the ~30 amino acid eukaryotic zinc finger motif in which a β-sheet and an α-helix are clustered around a zinc ion by various combinations of four ligands. The prokaryotic zinc finger domain (found in the Ros protein from Agrobacterium tumefaciens) is different from the eukaryotic counterpart as it consists of 58 amino acids arranged in a βββαα topology stabilized by a 15-residue hydrophobic core. Also, this domain tetrahedrally coordinates zinc and unfolds in the absence of the metal ion. The characterization of proteins belonging to the Ros homologs family has however shown that the prokaryotic zinc finger domain can overcome the metal requirement to achieve the same fold and DNA-binding activity. In the present work, two zinc-lacking Ros homologs (Ml4 and Ml5 proteins) have been thoroughly characterized using bioinformatics, biochemical and NMR techniques. We show how in these proteins a network of hydrogen bonds and hydrophobic interactions surrogate the zinc coordination role in the achievement of the same functional fold.
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy.
authors.forename: Ilaria
authors.initials: I
authors.lastname: Baglivo
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy.
authors.forename: Maddalena
authors.initials: M
authors.lastname: Palmieri
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy.
authors.forename: Alessia
authors.initials: A
authors.lastname: Rivellino
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy.
authors.forename: Fortuna
authors.initials: F
authors.lastname: Netti
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Russo
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Esposito
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy.
authors.forename: Rosa
authors.initials: R
authors.lastname: Iacovino
authors.affiliation: Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy.
authors.forename: Biancamaria
authors.initials: B
authors.lastname: Farina
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.
authors.forename: Carla
authors.initials: C
authors.lastname: Isernia
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Fattorusso
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.
authors.forename: Paolo Vincenzo
authors.initials: PV
authors.lastname: Pedone
authors.affiliation: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy. Electronic address: gaetano.malgieri@unina2.it.
authors.forename: Gaetano
authors.initials: G
authors.lastname: Malgieri
mesh_terms: D016960:Agrobacterium tumefaciens / Q000737:chemistry*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D002942:Circular Dichroism; D004247:DNA / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D008670:Metals / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D017386:Sequence Homology, Amino Acid; D016335:Zinc Fingers
chemical_list: D001426:Bacterial Proteins; D008670:Metals; D004247:DNA
keywords: DNA binding; Prokaryotic zinc finger; Thermal unfolding