Structures of DNA Polymerases Caught Processing Size‐Augmented Nucleotide Probes

Betz, Karin; Streckenbach, Frank; Schnur, Andreas; Exner, Thomas E.; Welte, Wolfram; Diederichs, Kay; Marx, Andreas

doi:10.1002/anie.200905724

Cited by 22 publications

(13 citation statements)

References 49 publications

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“…Abasic Site-All KlenTaq crystals grew in the same space group and very similar cell parameters (supplemental Table S1) as those reported earlier (19,20,35,(42)(43)(44)(45). Thus, significant differences in crystal packing forces acting on the active site should be negligible.…”

Section: Overall Structure Of Klentaq Complexes In Presence Of Anmentioning

confidence: 59%

Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites by a Family A DNA Polymerase

Obeid

Welte

Diederichs

et al. 2012

Journal of Biological Chemistry

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Background: Abasic sites are the most frequent DNA lesions and are often bypassed by incorporating an adenosine opposite that lesion. Results: We determined structures of DNA polymerase in complex with different nucleotides opposite an abasic site. Conclusion: Interaction of the incoming nucleotide with a single amino acid governs nucleotide selection opposite abasic sites. Significance: This work furthers the understanding of the bypass of a mutagenic lesion by DNA polymerases.

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Section: Overall Structure Of Klentaq Complexes In Presence Of Anmentioning

confidence: 59%

Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites by a Family A DNA Polymerase

Obeid

Welte

Diederichs

et al. 2012

Journal of Biological Chemistry

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“…For natural substrates the common sugar mostly observed is C3 0 -endo in the KlenTaq DNA polymerase active site. 23 The triphosphate moiety is very well defined in the electron density and interactions with polar residues of the O-helix allow the same stabilization as in the natural case (Fig. 3A and B).…”

mentioning

confidence: 77%

Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase

et al. 2017

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“…To facilitate comparison with other deposited structures, we also report resolution values at which 1/σ = 2 (see Table S1). Data reduction of the KTQ d 5SICS and KTQ d 5SICS -d NaM TP data was done in space group P3 1 21 (for cell dimensions see Table S1), and the structures were solved by rigid-body refinement using a previously published KlenTaq structure (PDB: 3M8S 49 ) as a model. All binary elongation complexes (KTQ(E1), KTQ(E2) and KTQ(E3)) crystallized in space group C222 1 with similar cell dimensions (see Table S1).…”

Section: Methodsmentioning

confidence: 99%

Structural Insights into DNA Replication without Hydrogen Bonds

et al. 2013

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The genetic alphabet is comprised of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the pre-chemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple post-chemistry complexes in which the already formed unnatural base pair is positioned at the post-insertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the post-insertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by de-intercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.

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Structures of DNA Polymerases Caught Processing Size‐Augmented Nucleotide Probes

Cited by 22 publications

References 49 publications

Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites by a Family A DNA Polymerase

Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites by a Family A DNA Polymerase

Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase

Structural Insights into DNA Replication without Hydrogen Bonds

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