Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium.
The crystal structure of the eubacteria Mycoplasma genitalium ORF MG438 polypeptide, determined by multiple anomalous dispersion and refined at 2.3 A 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 alpha-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.
Calisto
Bárbara M
BM
Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Josep-Samitier 1-5, 08028 Barcelona, Spain.
Pich
Oscar Q
OQ
Piñol
Jaume
J
Fita
Ignacio
I
Querol
Enrique
E
Carpena
Xavier
X
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D001483:Base Sequence; D018360:Crystallography, X-Ray; D015280:DNA Restriction-Modification Enzymes / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D045704:Mycoplasma genitalium / Q000201:enzymology* / Q000235:genetics; D020836:Protein Structure, Quaternary; D021122:Protein Subunits; D017386:Sequence Homology, Amino Acid; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000737:chemistry; D055672:Static Electricity
D001426:Bacterial Proteins; D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial; D021122:Protein Subunits; C059680:DNA modification methylase TaqI; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)