structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains

• Published in: Proceedings of the National Academy of Sciences - PNAS 2009-04, Vol.106 (17), p.6933-6938
• Main Authors: Baglivo, Ilaria, Russo, Luigi, Esposito, Sabrina, Malgieri, Gaetano, Renda, Mario, Salluzzo, Antonio, Di Blasio, Benedetto, Isernia, Carla, Fattorusso, Roberto, Pedone, Paolo V
• Format: Article
• Language: English
• Subjects: Agrobacterium tumefaciens; Alphaproteobacteria - chemistry; Alphaproteobacteria - genetics; Alphaproteobacteria - metabolism; Amino Acid Sequence; Amino acids; Bacterial proteins; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding sites; Biological Sciences; Cations; Chemical equilibrium; Coordinate systems; Coordination polymers; Cysteine; DNA; DNA-binding protein; Eukaryotes; Evolution; Fingers; Gene transfer; Heavy metals; Hydrophobic and Hydrophilic Interactions; Hydrophobicity; Ions; Mass Spectrometry; Mesorhizobium loti; Metals; Molecular Sequence Data; Molecular structure; Mutants; Mutation; Nuclear Magnetic Resonance, Biomolecular; Protein Binding; Protein Structure, Secondary; Proteins; Regulator genes; Sequence Alignment; Sequence Homology, Amino Acid; Structure-function relationships; Zinc; Zinc - chemistry; Zinc - metabolism; Zinc finger proteins; Zinc Fingers
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0810003106

The recent characterization of the prokaryotic Cys₂His₂ zinc-finger domain, identified in Ros protein from Agrobacterium tumefaciens, has demonstrated that, although possessing a similar zinc coordination sphere, this domain is structurally very different from its eukaryotic counterpart. A search in the databases has identified [almost equal to]300 homologues with a high sequence identity to the Ros protein, including the amino acids that form the extensive hydrophobic core in Ros. Surprisingly, the Cys₂His₂ zinc coordination sphere is generally poorly conserved in the Ros homologues, raising the question of whether the zinc ion is always preserved in these proteins. Here, we present a functional and structural study of a point mutant of Ros protein, Ros₅₆₋₁₄₂C82D, in which the second coordinating cysteine is replaced by an aspartate, 5 previously-uncharacterized representative Ros homologues from Mesorhizobium loti, and 2 mutants of the homologues. Our results indicate that the prokaryotic zinc-finger domain, which in Ros protein tetrahedrally coordinates Zn(II) through the typical Cys₂His₂ coordination, in Ros homologues can either exploit a CysAspHis₂ coordination sphere, previously never described in DNA binding zinc finger domains to our knowledge, or lose the metal, while still preserving the DNA-binding activity. We demonstrate that this class of prokaryotic zinc-finger domains is structurally very adaptable, and surprisingly single mutations can transform a zinc-binding domain into a nonzinc-binding domain and vice versa, without affecting the DNA-binding ability. In light of our findings an evolutionary link between the prokaryotic and eukaryotic zinc-finger domains, based on bacteria-to-eukaryota horizontal gene transfer, is discussed.