New insights into DNA polymerase mechanisms provided by time-lapse crystallography

Weaver, Tyler; Washington, M. Todd; Freudenthal, Bret

doi:10.1016/j.sbi.2022.102465

Cited by 2 publications

(2 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The thumb domain binds the double-stranded DNA, the fingers capture the incoming dNTP and the single-stranded template strand, and the palm contains the amino acids that coordinate two divalent metal cations essential for the chemical reaction [ 17 ]. The two metals have distinct roles and occupy different positions in the active center [ 18 ]. One serves as the catalytic metal at the so-called A site, and the other is the nucleotide metal at the B site.…”

Section: Metal Ions In Dna Polymerizationmentioning

confidence: 99%

For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases

Balint,

Unk

2023

IJMS

View full text Add to dashboard Cite

DNA polymerases constitute a versatile group of enzymes that not only perform the essential task of genome duplication but also participate in various genome maintenance pathways, such as base and nucleotide excision repair, non-homologous end-joining, homologous recombination, and translesion synthesis. Polymerases catalyze DNA synthesis via the stepwise addition of deoxynucleoside monophosphates to the 3′ primer end in a partially double-stranded DNA. They require divalent metal cations coordinated by active site residues of the polymerase. Mg2+ is considered the likely physiological activator because of its high cellular concentration and ability to activate DNA polymerases universally. Mn2+ can also activate the known DNA polymerases, but in most cases, it causes a significant decrease in fidelity and/or processivity. Hence, Mn2+ has been considered mutagenic and irrelevant during normal cellular function. Intriguingly, a growing body of evidence indicates that Mn2+ can positively influence some DNA polymerases by conferring translesion synthesis activity or altering the substrate specificity. Here, we review the relevant literature focusing on the impact of Mn2+ on the biochemical activity of a selected set of polymerases, namely, Polβ, Polλ, and Polµ, of the X family, as well as Polι and Polη of the Y family of polymerases, where congruous data implicate the physiological relevance of Mn2+ in the cellular function of these enzymes.

show abstract

Section: Metal Ions In Dna Polymerizationmentioning

confidence: 99%

For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases

Balint,

Unk

2023

IJMS

View full text Add to dashboard Cite

show abstract

“…Recently, with the application of advanced technologies, numerous and unexpected mechanistic features of DNA polymerases have been revealed, deepening our understanding of the structural mechanisms used by DNA polymerase. For example, time-lapse crystallography has revealed the binding of a third metal ion within the polymerase active site, the mechanisms of translocation along the DNA, the presence of new fidelity checkpoints and the mechanisms of pyrophosphorolysis [18]. Meanwhile, single-molecule F€ orster resonance energy transfer has deduced partially closed conformations and formulated a dynamic model depicting swiftly interchanging conformational populations influenced by complementarity [19].…”

Section: Introductionmentioning

confidence: 99%

Non‐canonical amino acids uncover the significant impact of Tyr671 on TaqDNA polymerase catalytic activity

Chen,

et al. 2024

The FEBS Journal

View full text Add to dashboard Cite

Responsible for synthesizing the complementary strand of the DNA template, DNA polymerase is a crucial enzyme in DNA replication, recombination and repair. A highly conserved tyrosine (Tyr), located at the C‐terminus of the O‐helix in family A DNA polymerases, plays a critical role in enzyme activity and fidelity. Here, we combined the technology of genetic code extension to incorporate non‐canonical amino acids and molecular dynamics (MD) simulations to uncover the mechanisms by which Tyr671 impacts substrate binding and conformation transitions in a DNA polymerase from Thermus aquaticus. Five non‐canonical amino acids, namely l‐3,4‐dihydroxyphenylalanine (l‐DOPA), p‐aminophenylalanine (pAF), p‐acetylphenylalanine (pAcF), p‐cyanophenylalanine (pCNF) and p‐nitrophenylalanine (pNTF), were individually incorporated at position 671. Strikingly, Y671pAF and Y671DOPA were active, but with lower activity compared to Y671F and wild‐type. Y671pAF showed a higher fidelity than the Y671F, despite both possessing lower fidelity than the wild‐type. Metadynamics and long‐timescale MD simulations were carried out to probe the role of mutations in affecting protein structure, including open conformation, open‐to‐closed conformation transition, closed conformation, and closed‐to‐open conformation transition. The MD simulations clearly revealed that the size of the 671 amino acid residue and interactions with substrate or nearby residues were critical for Tyr671 to determine enzyme activity and fidelity.

show abstract

New insights into DNA polymerase mechanisms provided by time-lapse crystallography

Cited by 2 publications

References 53 publications

For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases

For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases

Non‐canonical amino acids uncover the significant impact of Tyr671 on TaqDNA polymerase catalytic activity

Contact Info

Product

Resources

About