Sandbox 666: Difference between revisions
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== Structure == | == Structure == | ||
EcoRI is a homodimer, so it has two identical subunits (<scene name='Sandbox_666/Monomer_structure/3'>monomer strucure shown here</scene>)of 31 kDa, but it possible to have homotetramers at high concentrations.. The constitutive monomers are 276 amino acids long. EcoRI and all the other restriction enzymes show a common structural core which is a α/β domain. The constitutive subunits of EcoRI are organized into a single α/β domain (five stranded β sheet which are surrounded on by α helices). Four of these five β strands are parallel whereas the fourth (β4) is in an anti-parallel orientation to the others. | EcoRI is a homodimer, so it has two identical subunits (<scene name='Sandbox_666/Monomer_structure/3'>monomer strucure shown here</scene>) of 31 kDa, but it possible to have homotetramers at high concentrations.. The constitutive monomers are 276 amino acids long. EcoRI and all the other restriction enzymes show a common structural core which is a α/β domain. The constitutive subunits of EcoRI are organized into a single α/β domain (five stranded β sheet which are surrounded on by α helices). Four of these five β strands are parallel whereas the fourth (β4) is in an anti-parallel orientation to the others. | ||
The N-terminal section of each subunit forms, with a β-hairpin, an “arm” which wraps around the DNA molecule. (The arm brings the DNA molecule to the catalytic cleft.) | The N-terminal section of each subunit forms, with a β-hairpin, an “arm” which wraps around the DNA molecule. (The arm brings the DNA molecule to the catalytic cleft.) | ||
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The specific recognition of EcoRI 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, each residue form two hydrogen bonds with Guanine and the adjacent Adenosine residues respectively. | The specific recognition of EcoRI 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, 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/EXK motif. For EcoRI, this catalytic sequence is PD91 …E111AK.<scene name='Sandbox_666/Catalytic_core/3'>The catalytic core is shown here in red</scene> motif is also responsible for Mg2+ binding(Asp90 and Glu111). | The reaction is due to a catalytic sequence motif which is found in most type II restriction endonucleases: the PD…D/EXK motif. For EcoRI, this catalytic sequence is PD91 …E111AK.<scene name='Sandbox_666/Catalytic_core/3'>The catalytic core is shown here in red</scene>. This motif is also responsible for Mg2+ binding(Asp90 and Glu111). | ||
