Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda
Meredith C Foley1, Karunesh Arora, Tamar Schlick
1Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York, USA.
Biophysical Journal
|August 22, 2006
Summary
DNA polymerase lambda (pol lambda) undergoes subtle side-chain and DNA motions, not large subdomain shifts, to become chemistry-competent. These movements, influenced by active site ions and specific residues, are crucial for its DNA repair function.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- DNA polymerase lambda (pol lambda) is a low-fidelity enzyme in the X-family.
- It plays a role in DNA repair by filling short nucleotide gaps.
Purpose of the Study:
- To investigate the conformational transitions of pol lambda.
- To determine if pol lambda utilizes an induced-fit mechanism and an open-to-closed transition before catalytic activity.
Main Methods:
- Analysis of molecular dynamics simulations.
- Simulations conducted in binary and ternary states, with and without incoming nucleotide and catalytic Mg(2+) ions.
- Studies included active site residue mutants (Ile(492) and Arg(517)).
Main Results:
- Pol lambda does not exhibit large-scale subdomain motions like pol beta.
- Significant DNA motion and subtle side-chain movements were observed.
- Motions of specific residues (Ile(492), Tyr(505), Phe(506), Arg(514), Arg(517)) and DNA are coupled to active site ions.
- Enzyme closing occurred in an Ile(492)Ala mutant under specific conditions.
Conclusions:
- Pol lambda achieves a chemistry-competent state through sequential subtle motions, not large domain rearrangements.
- These motions are influenced by active site ions and specific residues, acting as gatekeepers for the reaction pathway.
- Identified residues and their motions are analogous to those in pol beta, suggesting conserved regulatory mechanisms.
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