Sandbox 666: Difference between revisions

In the old model the N-terminal section of each subunit forms the inner arm which wraps around the DNA molecule (The arm brings the DNA molecule to the catalytic cleft.).The new chain tracing, based on new elements of electron density and a new interpretation that alters the assignment of specific amino acid residues to some of the original features<ref name="B" />. In the new model,the inner arm is the extended chain motif (Met¹³⁷to Ala¹⁴²) is a segment of extended polypeptide chain that runs through the major groove of the DNA, roughly parallel to the DNA backbone<ref name="B" />. The outer arm is composed of two minor β strands linked together by a loop (the outer arm is 14 amino acids long, four of these amino acids belong to the loop).

The specific recognition of ''Eco''RI of the GAATTC sequence is mediated by twelve hydrogen bonds (six bonds per subunit) originating from α helical recognition modules. Three amino acids are responsible for the recognition:Arg²⁰⁰, Glu¹⁴⁴ and Arg¹⁴⁵. These aminoacids are shown in red <scene name='Sandbox_666/Grey_protein/3'>here</scene> .Each residue form two hydrogen bonds with Guanine and the adjacent Adenosine residues respectively.  

The reaction is due to a catalytic sequence motif which is found in most type II restriction endonucleases: the PD…(D/E)XK motif. For ''Eco''RI,<scene name='Sandbox_666/Catalytic_core/3'>this catalytic sequence</scene> is PD⁹¹ …E¹¹¹AK and the lysine residue is essential to the catalysis, but the proline residue is not important. This motif is also responsible for Mg2+ binding(Asp90 and Glu111).<ref>Structure and function of type II restriction endonucleases