1YDX

Crystal structure of Type-I restriction-modification system S subunit from M. genitalium

Summary for 1YDX

• Entry DOI: 10.2210/pdb1ydx/pdb
• Descriptor: type I restriction enzyme specificity protein MG438, CHLORIDE ION (3 entities in total)
• Functional Keywords: type-i hsds, dna binding protein
• Biological source: Mycoplasma genitalium
• Total number of polymer chains: 1
• Total formula weight: 47347.51

Authors

Machado, B.,Quijada, O.,Pinol, J.,Fita, I.,Querol, E.,Carpena, X. (deposition date: 2004-12-27, release date: 2005-08-23, Last modification date: 2024-11-20)

Primary citation

Calisto, B.M.,Pich, O.Q.,Pinol, J.,Fita, I.,Querol, E.,Carpena, X.
Crystal Structure of a Putative Type I Restriction-Modification S Subunit from Mycoplasma genitalium
J.Mol.Biol., 351:749-762, 2005

PubMed Abstract: 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.

PubMed: 16038930
DOI: 10.1016/j.jmb.2005.06.050

Experimental method

X-RAY DIFFRACTION (2.3 Å)