DNA Polymerases: Structural Diversity and Common Mechanisms

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Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution

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A general two-metal-ion mechanism for catalytic RNA

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Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA

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Structural basis for the 3′‐5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism.

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Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP

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STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP

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An attempt to unify the structure of polymerases

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FUNCTION AND STRUCTURE RELATIONSHIPS IN DNA POLYMERASES

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Structure–Function Studies of DNA Polymerase λ

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An Incoming Nucleotide Imposes an anti to syn Conformational Change on the Templating Purine in the Human DNA Polymerase-ι Active Site

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The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase

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Biochemistry of Magnesium

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Structure and mechanism of an intramembrane liponucleotide synthetase central for phospholipid biosynthesis

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Using structural motif templates to identify proteins with DNA binding function

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Protein-Template-Directed Synthesis across an Acrolein-Derived DNA Adduct by Yeast Rev1 DNA Polymerase

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Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D

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Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path

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Structural Mechanisms for Replicating DNA in Eukaryotes

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Activation of Trans Geometry in Bifunctional Mononuclear Platinum Complexes by a Piperidine Ligand

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Conformational Dynamics of DNA Polymerase Probed with a Novel Fluorescent DNA Base Analogue

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The p12 Subunit of Human Polymerase δ Modulates the Rate and Fidelity of DNA Synthesis

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Structure of Human DNA Polymerase κ Inserting dATP Opposite an 8-OxoG DNA Lesion

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A new paradigm of DNA synthesis: three-metal-ion catalysis

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Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I

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Insights into HIV-1 Reverse Transcriptase (RT) Inhibition and Drug Resistance from Thirty Years of Structural Studies

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Bumps in the road: how replicative DNA polymerases see DNA damage

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Y265H Mutator Mutant of DNA Polymerase β

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Exploring the Role of the Third Active Site Metal Ion in DNA Polymerase η with QM/MM Free Energy Simulations

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Enzyme screening with synthetic multifunctional pores: Focus on biopolymers

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Crystal structure of Cmr2 suggests a nucleotide cyclase‐related enzyme in type III CRISPR‐Cas systems

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An Unexplored Diversity of Reverse Transcriptases in Bacteria

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Mutations in human DNA polymerase η motif II alter bypass of DNA lesions

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Virus Evolution

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Cytotoxicity, cellular uptake, glutathione and DNA interactions of an antitumor large-ring PtII chelate complex incorporating the cis-1,4-diaminocyclohexane carrier ligand

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Automated Structural Comparisons Clarify the Phylogeny of the Right-Hand-Shaped Polymerases

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Polymerase-Directed Synthesis of 2‘-Deoxy-2‘-fluoro-β- D -arabinonucleic Acids

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Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation

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DNA Adduct Structure–Function Relationships: Comparing Solution with Polymerase Structures

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tRNA His guanylyltransferase catalyzes a 3′-5′ polymerization reaction that is distinct from G −1 addition

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Replication of UV-damaged DNA: new insights into links between DNA polymerases, mutagenesis and human disease

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Tuning DNA “strings”: Modulating the rate of DNA replication with mechanical tension

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Evolutionary innovations and the organization of protein functions in genotype space

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Interaction of DNA Polymerase I (Klenow Fragment) with the Single-Stranded Template beyond the Site of Synthesis

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Crystal structure of the Pyrococcus horikoshii DNA primase‐UTP complex: implications for the mechanism of primer synthesis

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tRNA His guanylyltransferase (THG1), a unique 3′-5′ nucleotidyl transferase, shares unexpected structural homology with canonical 5′-3′ DNA polymerases

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The Conserved Active Site Motif A of Escherichia coliDNA Polymerase I Is Highly Mutable

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Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly

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Common structural features of nucleic acid polymerases

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Current Developments in HIV Chemotherapy

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RB69 DNA Polymerase Structure, Kinetics, and Fidelity

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Bioinformatics and Molecular Modeling in Chemical Enzymology. Active Sites of Hydrolases

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A proposal: Evolution of PCNA's role as a marker of newly replicated DNA

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The Replication System of Bacteriophage T7

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Plant organellar DNA polymerases are replicative and translesion DNA synthesis polymerases

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Oxidation of Thymine to 5-Formyluracil in DNA Promotes Misincorporation of dGMP and Subsequent Elongation of a Mismatched Primer Terminus by DNA Polymerase

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Structural insights into eukaryotic DNA replication

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Quasispecies structure, cornerstone of hepatitis B virus infection: Mass sequencing approach

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Mechanism of allosteric inhibition of HIV-1 reverse transcriptase revealed by single-molecule and ensemble fluorescence

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DNA Polymerases and Aminoacyl-tRNA Synthetases: Shared Mechanisms for Ensuring the Fidelity of Gene Expression

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Acidic Residues Critical for the Activity and Biological Function of Yeast DNA Polymerase η

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HCV Genetic Variability: From Quasispecies Evolution to Genotype Classification

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Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases

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Significance of Nucleobase Shape Complementarity and Hydrogen Bonding in the Formation and Stability of the Closed Polymerase−DNA Complex

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Electronic Measurements of Single-Molecule Processing by DNA Polymerase I (Klenow Fragment)

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Conformation, protein recognition and repair of DNA interstrand and intrastrand cross-links of Antitumor trans-[PtCl2(NH3)(thiazole)]

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Target Recognition by Catechols and β-Ketoenols: Potential Contribution of Hydrogen Bonding and Mn/Mg Chelation to HIV-1 Integrase Inhibition

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Structural mechanism of LINE-1 target-primed reverse transcription

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PCNA accelerates the nucleotide incorporation rate by DNA polymerase δ

Mondol, T., Stodola, J. L., Galletto, R., & Burgers, P. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1321 · Cited by 43

Structure and Function of RNA Polymerase II

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Substrate-induced Conformational Fit and Headpiece Closure in the Ca2+ATPase (SERCA)

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Quantum Mechanics/Molecular Mechanics Investigation of the Chemical Reaction in Dpo4 Reveals Water-Dependent Pathways and Requirements for Active Site Reorganization

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Structural Comparison of DNA Polymerase Architecture Suggests a Nucleotide Gateway to the Polymerase Active Site

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A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli

Sharma, A. S., Kottur, J., Narayanan, N., & Nair, D. T. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt146 · Cited by 42

Programmed Allelic Mutagenesis of a DNA Polymerase with Single Amino Acid Resolution

Nikoomanzar, A., Vallejo, D., Yik, E. J., & Chaput, J. C. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00236 · Cited by 42

Characterization of the 2-Phospho- l -lactate Transferase Enzyme Involved in Coenzyme F420 Biosynthesis in Methanococcus jannaschii

Graupner, M., Xu, H., & White, R. H. (2002) · Biochemistry · doi:10.1021/bi011937v · Cited by 42

In Vivo Mutagenesis by Escherichia coliDNA Polymerase I

Shinkai, A., & Loeb, L. A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m104780200 · Cited by 42

Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases

Seifert, M., van Nies, P., Papini, F. S., Arnold, J. J., Poranen, M. M., Cameron, C. E., Depken, M., & Dulin, D. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa233 · Cited by 40

Recent Insight into the Kinetic Mechanisms and Conformational Dynamics of Y-Family DNA Polymerases

Maxwell, B. A., & Suo, Z. (2014) · Biochemistry · doi:10.1021/bi5000405 · Cited by 41

RNA-dependent RNA polymerases of dsRNA bacteriophages

Makeyev, E. V., & Grimes, J. M. (2004) · Virus Research · doi:10.1016/j.virusres.2003.12.005 · Cited by 40

The Eukaryotic Replication Machine

Zhang, D., & O’Donnell, M. E. (2016) · The Enzymes · doi:10.1016/bs.enz.2016.03.004 · Cited by 39

Regulation and Modulation of Human DNA Polymerase δ Activity and Function

Lee, M., Wang, X., Zhang, S., Zhang, Z., & Lee, E. (2017) · Genes · doi:10.3390/genes8070190 · Cited by 42

Conservative transcription in three steps visualized in a double-stranded RNA virus

Cui, Y., Zhang, Y., Zhou, K., Sun, J., & Zhou, Z. H. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0320-0 · Cited by 41

Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases

Stagno, J. R., Aphasizheva, I., Aphasizhev, R., & Luecke, H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704259104 · Cited by 41

Crystallographic Analysis of a Novel Complex of Actinomycin D Bound to the DNA Decamer CGATCGATCG

Robinson, H. H., Gao, Y., Yang, X., Sanishvili, R., Joachimiak, A., & Wang, A. H. ‐. (2001) · Biochemistry · doi:10.1021/bi002859z · Cited by 41

Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen

Perlow, R. A., & Broyde, S. B. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4674 · Cited by 41

Human DNA Polymerase η Is Pre-Aligned for dNTP Binding and Catalysis

Ummat, A., Silverstein, T. D., Jain, R., Buku, A., Johnson, R. E., Prakash, L., Prakash, S., & Aggarwal, A. K. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.11.038 · Cited by 40

Structural and Molecular Kinetic Features of Activities of DNA Polymerases

Кузнецова, А. А., Fedorova, O. S., & Kuznetsov, N. A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23126373 · Cited by 41

Dynamic mechanism of nick recognition by DNA ligase

Cherepanov, A. V., & de Vries, S. (2002) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2002.03309.x · Cited by 40

RNA-editing Terminal Uridylyl Transferase 1

Aphasizheva, I., Aphasizhev, R., & Simpson, L. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m401234200 · Cited by 40

Effect of manganese on in vitro replication of damaged DNA catalyzed by the herpes simplex virus type-1 DNA polymerase

Villani, G. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf463 · Cited by 40

A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation

Da, L., Chao, E., Duan, B., Zhang, C., Zhou, X., & Yu, J. H. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004624 · Cited by 40

Computer simulation studies of the fidelity of DNA polymerases

Florián, J., Goodman, M. F., & Warshel, A. (2003) · Biopolymers · doi:10.1002/bip.10244 · Cited by 40

A Ligand-observed Mass Spectrometry Approach Integrated into the Fragment Based Lead Discovery Pipeline

Chen, X., Qin, S., Chen, S., Li, J., Li, L., Wang, Z., Wang, Q., Lin, J., Yang, C., & Shui, W. (2015) · Scientific Reports · doi:10.1038/srep08361 · Cited by 41

Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion

Lior-Hoffmann, L., Wang, L., Wang, S., Geacintov, N. E., Broyde, S. B., & Zhang, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks653 · Cited by 39

Therminator DNA Polymerase: Modified Nucleotides and Unnatural Substrates

Gardner, A. F., Jackson, K. M., Boyle, M. M., Buss, J. A., Potapov, V., Gehring, A. M., Zatopek, K. M., Junior, I. R. C., Ong, J. L., & Jack, W. E. (2019) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00028 · Cited by 42

Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex

Rungrotmongkol, T., Mulholland, A. J., & Hannongbua, S. (2006) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2006.09.004 · Cited by 39

Comparative Kinetics of Nucleotide Analog Incorporation by Vent DNA Polymerase

Gardner, A. F., Joyce, C. M., & Jack, W. E. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m308286200 · Cited by 39

Functional Analysis of RNA Binding by the Hepatitis C Virus RNA-dependent RNA Polymerase

Kim, Y. C., Russell, W. K., Ranjith-Kumar, C. T., Thomson, M., Russell, D. H., & Kao, C. C. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m508145200 · Cited by 38

Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates

Zhang, H., Cao, W., Zakharova, E., Konigsberg, W. H., & Cruz, E. M. D. L. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm587 · Cited by 38

A Quantum Mechanical Investigation of Possible Mechanisms for the Nucleotidyl Transfer Reaction Catalyzed by DNA Polymerase β

Bojin, M. D., & Tamar Schlick, A. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp071838c · Cited by 38

Human DNA polymerase α in binary complex with a DNA:DNA template-primer

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Molecular insights into NRTI inhibition and mitochondrial toxicity revealed from a structural model of the human mitochondrial DNA polymerase

Bienstock, R. J., & Copeland, W. C. (2004) · Mitochondrion · doi:10.1016/j.mito.2004.05.018 · Cited by 38

Following replicative DNA synthesis by time-resolved X-ray crystallography

Chim, N., Meza, R. A., Trinh, A. M., Yang, K., & Chaput, J. C. (2021) · Nature Communications · doi:10.1038/s41467-021-22937-z · Cited by 34

Single-Molecule Study of DNA Polymerization Activity of HIV-1 Reverse Transcriptase on DNA Templates

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The three-component helicase/primase complex of herpes simplex virus-1

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