Table 3.
pol μ | pol β | pol λ | pol X | Function in pol μ | Function in other polymerases |
---|---|---|---|---|---|
Asp330 | Asp190 | Asp427 | Asp49 | Coordinates with Mg2+ for chemical reaction | Coordinates with Mg2+ for chemical reaction |
Asp332 | Asp192 | Asp429 | Asp51 | Coordinates with Mg2+ for chemical reaction | Coordinates with Mg2+ for chemical reaction |
Asp420 | Asp256 | Asp490 | Asp100 | Coordinates with Mg2+ for chemical reaction | Coordinates with Mg2+ for chemical reaction |
His329 | Gly189 | Gly426 | Asn48 | Flips to trigger the flip of Asp330 | |
Gly435 | Tyr271 | Tyr505 | His115 | Contacts DNA bases, thereby correctly positioning the primer terminus for catalysis | |
Trp436 | Phe272 | Phe506 | Phe116 | Flips to initiate DNA or subdomain motion | |
Val422 | Arg258 | Ile492 | Phe102 | Interacts with other key residues to control their conformational change | |
Gln440 | Asp276 | Ala510 | Val120 | Participates in accommodating the incoming nucleotide | Weakens the binding affinity with the nucleotide (pol β) |
Glu443 | Asn279 | Asn513 | Leu123 | Participate in accommodating the incoming nucleotide through water | Hydrogen-bonds to the nucleotide and is directly related to catalytic ability (pol β) |
Arg444 | Lys280 | Arg514 | Ile124 | Stabilizes DNA in closed form by stacking with the template | First residue to respond to thumb motion (pol λ) stacks with template base in closed state |
Arg447 | Arg283 | Arg517 | Arg127 | Stabilizes the DNA template and Loop 1 in closed form | Stabilizes DNA in closed form and helps check for correct basepairing |
Arg448 | Ala284 | Ala518 | Ala128 | Stabilizes DNA to prevent insertion errors; stabilizes Loop 1 in closed form |
∗Residues in bold indicate motion detected in wild-type MD simulations.