Crystal Structure of a Putative Type I Restriction–Modification S Subunit from Mycoplasma genitalium

• Published in: Journal of molecular biology 2005-08, Vol.351 (4), p.749-762
• Main Authors: Calisto, Bárbara M., Pich, Oscar Q., Piñol, Jaume, Fita, Ignacio, Querol, Enrique, Carpena, Xavier
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Base Sequence; crystal structure; Crystallography, X-Ray; DNA recognition; DNA Restriction-Modification Enzymes - chemistry; DNA Restriction-Modification Enzymes - classification; DNA Restriction-Modification Enzymes - genetics; DNA, Bacterial - genetics; HsdS; Models, Molecular; Molecular Sequence Data; Mycoplasma genitalium; Mycoplasma genitalium - enzymology; Mycoplasma genitalium - genetics; Protein Structure, Quaternary; Protein Subunits; Sequence Homology, Amino Acid; Site-Specific DNA-Methyltransferase (Adenine-Specific) - chemistry; Static Electricity; Type I restriction and modification system
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2005.06.050

The crystal structure of the eubacteria Mycoplasma genitalium ORF MG438 polypeptide, determined by multiple anomalous dispersion and refined at 2.3 Å resolution, reveals the organization of S subunits from the Type I restriction and modification system. The structure consists of two globular domains, with about 150 residues each, separated by a pair of 40 residue long antiparallel α-helices. The globular domains correspond to the variable target recognition domains (TRDs), as previously defined for S subunits on sequence analysis, while the two helices correspond to the central (CR1) and C-terminal (CR2) conserved regions, respectively. The structure of the MG438 subunit presents an overall cyclic topology with an intramolecular 2-fold axis that superimposes the N and the C-half parts, each half containing a globular domain and a conserved helix. TRDs are found to be structurally related with the small domain of the Type II N6-adenine DNA MTase TaqI. These relationships together with the structural peculiarities of MG438, in particular the presence of the intramolecular quasi-symmetry, allow the proposal of a model for S subunits recognition of their DNA targets in agreement with previous experimental results. In the crystal, two subunits of MG438 related by a crystallographic 2-fold axis present a large contact area mainly involving the symmetric interactions of a cluster of exposed hydrophobic residues. Comparison with the recently reported structure of an S subunit from the archaea Methanococcus jannaschii highlights the structural features preserved despite a sequence identity below 20%, but also reveals important differences in the globular domains and in their disposition with respect to the conserved regions.