Sandbox 666: Difference between revisions
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== Structure == | == Structure == | ||
In the CDD (Conserved Domain Database, almost the entire sequence of EcoRI contains a conserved domain which is the EcoRI Superfamily. | |||
EcoRI is a homodimer, so it has two identical subunits (Representation of one <scene name='Sandbox_666/Monomer_structure/4'>subunit</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 <scene name='Sandbox_666/B_sheet/1'>β</scene> sheet which is surrounded by <scene name='Sandbox_666/Helix/1'>α helices</scene> ). Four of these five β strands are parallel whereas the fourth (β4) is in an anti-parallel orientation to the others.<ref>Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. | EcoRI is a homodimer, so it has two identical subunits (Representation of one <scene name='Sandbox_666/Monomer_structure/4'>subunit</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 <scene name='Sandbox_666/B_sheet/1'>β</scene> sheet which is surrounded by <scene name='Sandbox_666/Helix/1'>α helices</scene> ). Four of these five β strands are parallel whereas the fourth (β4) is in an anti-parallel orientation to the others.<ref>Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. | ||
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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 anew interpretation that alters the assignment of specific amino acid residues to some of the original features<ref>Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. | |||
Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM.</ref>. In the new model,the Inner arm is the extended chain motif (Met<sup>137</sup>to Ala<sup>142</sup>)is a segment of extended polypeptide chain that runs through the major groove of the DNA, roughly parallel to the DNA backbone<ref>Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. | |||
Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM.</ref>. 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). | |||
