Sandbox 666: Difference between revisions
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== Structure == | == Structure == | ||
{{STRUCTURE_1eri| PDB=1eri | SCENE= | size='500'}} | |||
{{STRUCTURE_1eri| PDB=1eri | SCENE= | size='500'}} | |||
''Eco''RI is composed of two homodimers, so it has two identical subunits (Representation of one <scene name='Sandbox_666/Monomer_structure/4'>subunit</scene>) of 31 kDa, but it is possible to have homotetramers at high concentrations. The constitutive monomers are 276 amino acids long. ''Eco''RI and all the other restriction enzymes show a common structural core, which is a α/β domain. There are several non-contiguous structural elements, whose are involved in DNA recognition<ref name="A">. The constitutive subunits of ''Eco''RI are organized into a single α/β domain (five strands <scene name='Sandbox_666/B_sheet/1'>β</scene> sheet, which is surrounded by <scene name='Sandbox_666/Helix/1'>two 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 name="B">Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. | ''Eco''RI is composed of two homodimers, so it has two identical subunits (Representation of one <scene name='Sandbox_666/Monomer_structure/4'>subunit</scene>) of 31 kDa, but it is possible to have homotetramers at high concentrations. The constitutive monomers are 276 amino acids long. ''Eco''RI and all the other restriction enzymes show a common structural core, which is a α/β domain. There are several non-contiguous structural elements, whose are involved in DNA recognition<ref name="A">. The constitutive subunits of ''Eco''RI are organized into a single α/β domain (five strands <scene name='Sandbox_666/B_sheet/1'>β</scene> sheet, which is surrounded by <scene name='Sandbox_666/Helix/1'>two 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 name="B">Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. | ||
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Journal: (1990) Science 249: 1307-1309 </ref>. Four helices (two of each subunit) recognize the major groove and bring residues, whose interact with DNA bases and backbones. | Journal: (1990) Science 249: 1307-1309 </ref>. Four helices (two of each subunit) recognize the major groove and bring residues, whose interact with DNA bases and backbones. | ||
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). In the recent model, the extended chain motif ('''Met<sup>137</sup> to Ala<sup>142</sup>''') is a segment of the extended polypeptide chain, which runs through the major groove of the DNA, roughly parallel to the DNA backbone<ref name="B" /> and forms the specific contacts of the enzymes to the DNA. 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). | 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). In the recent model, the extended chain motif ('''Met<sup>137</sup> to Ala<sup>142</sup>''') is a segment of the extended polypeptide chain, which runs through the major groove of the DNA, roughly parallel to the DNA backbone<ref name="B" /> and forms the specific contacts of the enzymes to the DNA. 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). | ||
