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DNA Pol S&F
Description of the structure and function of the T7 DNA Polymerase
| Question | Answer |
|---|---|
| Who discovered the first DNA Pol? When? | Arthur Kornberg, 1956 |
| Directionality of DNA replication? | 5'-->3' |
| 2 main functions of DNA Polymerase? | -Fidelity of DNA replication -Ligation of dNTPs to primer strand |
| What factors affect the fidelity of DNA replication? | -Selection of the correct dNTP based on the template strand -Excision of incorrect bases by the exonuclease activity of the polymerase |
| What is processivity? | The ability of an enzyme to complete several catalytic cycles without dissociating from its substrate |
| What is the overall architecture of the T7 DNA Polymerase? | The shape of a right hand with fingers, palm, and thumb domains |
| What domain contributes to the processivity of the enzyme? | Thioredoxin domain |
| What metal ions are most likely involved in DNA Polymerization? How many of them are there? | Mg2+, 2 |
| Where is the DNA-binding groove located? | Between the fingers, thumb, and palm domains |
| Which domain is found at the N-terminus of the protein? | Exonuclease |
| Which domain is found at the C-terminus of the protein/ | Polymerase |
| Where is the thioredoxin domain located? | On top of the thumb |
| What strictly conserved residues are necessary for enzyme function? Where are they located? | -3 acidic residues (Asp475, Asp654, Glu655) -In the active site in the DNA-binding groove |
| What does the B-factor of the active site tell us about the region around the active site of the protein? | there is little to no movement in this area to ensure affinity for DNA |
| What is the Klenow fragment? | The historical name for the part of the enzyme that contains catalytic activity. |
| What domains are present in the Klenow fragment? | The polymerase and exonuclease domains |
| What enzyme was used to isolate the klenow fragment? | Subtilisin |
| What purpose does the thioredoxin domain play in DNA replication? | Provides processivity to the activity of DNA Polymerase |
| Where does polymerization occur? | At the confluence of the fingers and the palm domains |
| What interactions stabilize the enzyme-DNA complex? | Electrostatic interactions with the PO4 backbone |
| Why does the enzyme interact with the phosphate backbone? | To avoid sequence-dependent interaction with DNA that would hinder processivity |
| What shape is the helical axis of the primer-template heteroduplex DNA? What causes this? | The heteroduplex DNA adopts an S-shape due to extensive interaction with the thumb and fingers domains |
| Is t he heteroduplex DNA in A- or B-form? | No. It is slightly contorted so that the minor groove is widened relative to B-DNA. |
| What role does His607 play in the activity of the enzyme? | Base-stacks with the template base to hold it in optimal configuration for base-pairing with the incoming dNTP |
| What effect does template distortion have? | Positions the template base to Watson-Crick base-pair with the incoming dNTP. |
| How do the authors account for the higher-than-expected fidelity of the enzyme? | The active site is shielded from water, increasing the dielectric constant of the environment |
| What factors contribute to exclude water from the active site? | -The O-helix of the fingers domain, Tyr526, and the 3' base of the primer |
| What stabilizes the incoming dNTP? | The helical dipole of the L-helix is oriented such that the negative charge of the triphosphate group of the incoming NTP is stabilized |
| Why is the solved complex considered non-covalent? | The most recently incorporated base is a ddNTP which does not allow incorporation of the next base. |
| What is the mechanism by which the incoming dNTP is ligated to the primer strand? | DNA polymerases catalyze the phosphoryl transfer through nucleophilic attack of the primer 3' hydroxyl on the alpha-phosphate of a dNTP |
| How do DNA polymerases discriminate so heavily against the incorporation of RNTPs? | Realistically, we don't know. However, the authors suggest the presence of a hydrophobic pocket formed by Tyr526 and the aliphatic part of the side chain of Glu480. Glu480 is held in place by Tyr530. This pocket excludes the RNTP 2' hydroxyl |
| Which step of the catalytic cycle does the solved structure represent? | The authors propose that the complex is in the activated transition state. |
Created by:
mbell133
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