An open and closed case for all polymerases
Open accessAbstract
The recently determined structures of HIV-1 reverse transcriptase and Taq DNA polymerase in complex with DNA primer-template and an incoming nucleotide have shown that a large conformational change configures the polymerase active site for nucleotidyl transfer. The structure of reverse transcriptase in the catalytic complex will open the path to the rational design of novel nucleoside analog inhibitors of viral replication.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Crystal structures reveal that polymerase binding to DNA strongly reshapes the primer-template, for example the backbone at the templating base can be bent by 90°.
“Crystal structures (Refs.15-22 and references therein) reveal that polymerase binding to DNA strongly reshapes the primertemplate, e.g. the backbone at the templating base can be bent by 90°.”
From DNA Replication Fidelity (2004) · cites this paper as [18]
Polymerases in families A, B, X, and RT have nascent base pair binding pockets that tightly accommodate a correct Watson-Crick base pair.
“Polymerases in families A, B, X, and RT have nascent base pair binding pockets that tightly accommodate a correct Watson-Crick base pair (Fig. 2A and additional images in Refs.15-19 and references therein).”
From DNA Replication Fidelity (2004) · cites this paper as [18]
Cites
Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor
Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A., & Steitz, T. A. (1992) · Science · doi:10.1126/science.1377403 · Cited by 1,914 · see citing works
Huang, H., Chopra, R., Verdine, G. L., & Harrison, S. C. (1998) · Science · doi:10.1126/science.282.5394.1669 · Cited by 1,420 · see citing works
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
Doublié, S., Tabor, S., Long, A. M., Richardson, C. C., & Ellenberger, T. (1998) · Nature · doi:10.1038/34593 · Cited by 1,177 · see citing works
Self-citationJacobo-Molina, A., Ding, J., Nanni, R. G., Clark, A. D., Lu, X., Tantillo, C., Williams, R. L., Kamer, G., Ferris, A. L., Clark, P., et al. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.13.6320 · Cited by 1,115 · see citing works
Beese, L. S., & Steitz, T. A. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07917.x · Cited by 1,051 · see citing works
Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
Ollis, D. L., Brick, P., Hamlin, R. C., Xuong, N., & Steitz, T. A. (1985) · Nature · doi:10.1038/313762a0 · Cited by 848 · see citing works
STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP
Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., & Kraut, J. (1994) · Worldwide Protein Data Bank · doi:10.2210/pdb2bpf/pdb · Cited by 694 · see citing works
Self-citationLi, Y., Korolev, S., & Waksman, G. (1998) · The EMBO Journal · doi:10.1093/emboj/17.24.7514 · Cited by 689 · see citing works
An attempt to unify the structure of polymerases
Delarue, M. H., Poch, O., Tordo, N., Moras, D., & Argos, P. (1990) · Protein Engineering Design and Selection · doi:10.1093/protein/3.6.461 · Cited by 638 · see citing works
Structures of Ternary Complexes of Rat DNA Polymerase β, a DNA Template-Primer, and ddCTP
Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., & Kraut, J. (1994) · Science · doi:10.1126/science.7516580 · Cited by 598 · see citing works
Self-citationSawaya, M. R., Prasad, R., Wilson, S. H., Kraut, J., & Pelletier, H. (1997) · Biochemistry · doi:10.1021/bi9703812 · Cited by 593 · see citing works
Self-citationMechanism of Inhibition of HIV-1 Reverse Transcriptase by Nonnucleoside Inhibitors
Spence, R., Kati, W. M., Anderson, K. S., & Johnson, K. A. (1995) · Science · doi:10.1126/science.7532321 · Cited by 522 · see citing works
Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
Kiefer, J. R., Mao, C., Braman, J. C., & Beese, L. S. (1998) · Nature · doi:10.1038/34693 · Cited by 518 · see citing works
High resolution structures of HIV-1 RT from four RT–inhibitor complexes
Ren, J., Esnouf, R. M., Garman, E. F., Somers, D. O., Ross, C., Kirby, I., Keeling, J., Darby, G. K., Jones, E. Y., Stuart, D. I., et al. (1995) · Nature Structural & Molecular Biology · doi:10.1038/nsb0495-293 · Cited by 503 · see citing works
Crystal Structure of Rat DNA Polymerase β: Evidence for a Common Polymerase Mechanism
Sawaya, M. R., Pelletier, H., Kumar, A., Wilson, S. H., & Kraut, J. (1994) · Science · doi:10.1126/science.7516581 · Cited by 469 · see citing works
Self-citationMechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors
Esnouf, R. M., Ren, J., Ross, C., Jones, E. Y., STAMMERS, D. K., & Stuart, D. I. (1995) · Nature Structural & Molecular Biology · doi:10.1038/nsb0495-303 · Cited by 442 · see citing works
Crystal Structure of a pol α Family Replication DNA Polymerase from Bacteriophage RB69
Wang, J., Sattar, A. K. M. A., Wang, C. C., Karam, J. D., Konigsberg, W. H., & Steitz, T. A. (1997) · Cell · doi:10.1016/s0092-8674(00)80296-2 · Cited by 430 · see citing works
Wong, I., Patel, S. S., & Johnson, K. A. (1991) · Biochemistry · doi:10.1021/bi00216a030 · Cited by 366 · see citing works
Crystal structure of Thermus aquaticus DNA polymerase
Kim, Y., Eom, S. H., Wang, J., Lee, D., Suh, S. W., & Steitz, T. A. (1995) · Nature · doi:10.1038/376612a0 · Cited by 360 · see citing works
Structure of Taq polymerase with DNA at the polymerase active site
Eom, S. H., Wang, J., & Steitz, T. A. (1996) · Nature · doi:10.1038/382278a0 · Cited by 331 · see citing works
Korolev, S., Nayal, M., Barnes, W. M., Di, E., & Waksman, G. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.20.9264 · Cited by 171 · see citing works
Crystal structure of a thermostable Bacillus DNA polymerase l large fragment at 2.1 Å resolution
Kiefer, J. R., Mao, C., Hansen, C., Basehore, S. L., Hogrefe, H. H., Braman, J. C., & Beese, L. S. (1997) · Structure · doi:10.1016/s0969-2126(97)00169-x · Cited by 162 · see citing works
Georgiadis, M. M., Jessen, S. M., Ogata, C. M., Telesnitsky, A., Goff, S. P., & Hendrickson, W. A. (1995) · Structure · doi:10.1016/s0969-2126(01)00223-4 · Cited by 149 · see citing works
A minor groove binding track in reverse transcriptase
Bębenek, K., Beard, W. A., Darden, T. A., Li, L., Prasad, R., Luxon, B. A., Gorenstein, D. G., Wilson, S. H., & Kunkel, T. A. (1997) · Nature Structural Biology · doi:10.1038/nsb0397-194 · Cited by 111 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Kunkel, T. A., & Bebenek, K. (2000) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.69.1.497 · Cited by 1,003 · see citing works
Miller, E. S., Kutter, E. M., Mosig, G., Arisaka, F., Kunisawa, T., & Rüger, W. (2003) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.67.1.86-156.2003 · Cited by 818 · see citing works
Kunkel, T. A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.r400006200 · Cited by 754 · see citing works
Weber, P. C., Lesburg, C. A., Cable, M., Ferrari, E., Hong, Z., & Mannarino, A. F. (1999) · Nature Structural Biology · doi:10.1038/13305 · Cited by 738 · see citing works
Crystal Structure of a Y-Family DNA Polymerase in Action
Ling, H., Boudsocq, F., Woodgate, R., & Yang, W. (2001) · Cell · doi:10.1016/s0092-8674(01)00515-3 · Cited by 610 · see citing works
STRUCTURAL INSIGHTS INTO TRANSLATIONAL FIDELITY
Ogle, J. M., & Ramakrishnan, V. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.061903.155440 · Cited by 586 · see citing works
Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus
Bressanelli, S., Tomei, L., Roussel, A., Incitti, I., Vitale, R., Mathieu, M., Francesco, R. D., & Rey, F. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.23.13034 · Cited by 587 · see citing works
Making and Breaking Nucleic Acids: Two-Mg2+-Ion Catalysis and Substrate Specificity
Yang, W., Lee, J. Y., & Nowotny, M. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.03.013 · Cited by 573 · see citing works
Structure of the Replicating Complex of a Pol α Family DNA Polymerase
Franklin, M. C., Wang, J., & Steitz, T. A. (2001) · Cell · doi:10.1016/s0092-8674(01)00367-1 · Cited by 538 · see citing works
Protein factors in pre-mRNA 3′-end processing
Mandel, C. R., Bai, Y., & Tong, L. (2007) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-007-7474-3 · Cited by 415 · see citing works
Directed evolution of polymerase function by compartmentalized self-replication
Ghadessy, F. J., Ong, J. L., & Holliger, P. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.071052198 · Cited by 398 · see citing works
Structure of the Catalytic Core of S. cerevisiae DNA Polymerase η
Trincão, J., Johnson, R. E., Escalante, C. R., Prakash, S., Prakash, L., & Aggarwal, A. K. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00306-9 · Cited by 344 · see citing works
DNA Polymerase Fidelity: Kinetics, Structure, and Checkpoints
Joyce, C. M., & Benkovic, S. J. (2004) · Biochemistry · doi:10.1021/bi048422z · Cited by 318 · see citing works
RNA Synthesis in a Cage—Structural Studies of Reovirus Polymerase λ3
Tao, Y. J., Farsetta, D. L., Nibert, M. L., & Harrison, S. C. (2002) · Cell · doi:10.1016/s0092-8674(02)01110-8 · Cited by 318 · see citing works
Two-Metal-Ion Catalysis in Adenylyl Cyclase
Tesmer, J. J. G., Sunahara, R. K., Johnson, R. A., Gosselin, G., Gilman, A. G., & Sprang, S. R. (1999) · Science · doi:10.1126/science.285.5428.756 · Cited by 306 · see citing works
Structures of Mismatch Replication Errors Observed in a DNA Polymerase
Johnson, S. J., & Beese, L. S. (2004) · Cell · doi:10.1016/s0092-8674(04)00252-1 · Cited by 300 · see citing works
Structure and Mechanism of DNA Polymerase β
Beard, W. A., & Wilson, S. H. (2006) · Chemical Reviews · doi:10.1021/cr0404904 · Cited by 299 · see citing works
Johnson, S. J., Taylor, J. S., & Beese, L. S. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0630532100 · Cited by 289 · see citing works
Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism
Yang, W., & Gao, Y. (2018) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-062917-012405 · Cited by 245 · see citing works
Delarue, M. H., & Sanejouand, Y. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00562-4 · Cited by 246 · see citing works
Conformational transitions in DNA polymerase I revealed by single-molecule FRET
Santoso, Y., Joyce, C., Potapova, O., Reste, L. L., Hohlbein, J., Torella, J., Grindley, N. D., & Kapanidis, A. (2009) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0910909107 · Cited by 238 · see citing works
Telomerase Mechanism of Telomere Synthesis
Wu, R. A., Upton, H. E., Vogan, J. M., & Collins, K. (2017) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061516-045019 · Cited by 208 · see citing works
Structure-Function Relationships Among RNA-Dependent RNA Polymerases
Ng, K. K.-S., Arnold, J. J., & Cameron, C. E. (2007) · Current topics in microbiology and immunology · doi:10.1007/978-3-540-75157-1_7 · Cited by 215 · see citing works
Structural basis for the dual coding potential of 8‐oxoguanosine by a high‐fidelity DNA polymerase
Brieba, L. G., Eichman, B. F., Kokoska, R. J., Doublié, S., Kunkel, T. A., & Ellenberger, T. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600354 · Cited by 210 · see citing works
Self-citationNon-nucleoside Analogue Inhibitors Bind to an Allosteric Site on HCV NS5B Polymerase
Wang, M., Ng, K. K.-S., Cherney, M. M., Chan, L. C., Yannopoulos, C. G., Bedard, J., Morin, N., Nguyen‐Ba, N., Alaoui-Ismaili, M. H., Bethell, R. C., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m209397200 · Cited by 194 · see citing works
Snapshots of Replication through an Abasic Lesion
Ling, H., Boudsocq, F., Woodgate, R., & Yang, W. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00101-7 · Cited by 186 · see citing works
Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis
Vaisman, A., Ling, H., Woodgate, R., & Yang, W. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600786 · Cited by 182 · see citing works
Supra-domains: Evolutionary Units Larger than Single Protein Domains
Vogel, C., Berzuini, C., Bashton, M., Gough, J., & Teichmann, S. A. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.12.026 · Cited by 181 · see citing works
Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus.
Silvian, L. F., Toth, E. A., Pham, P., Goodman, M. F., & Ellenberger, T. E. (2001) · Nature Structural Biology · doi:10.1038/nsb1101-984 · Cited by 179 · see citing works
Self-citationAn Overview of Y-Family DNA Polymerases and a Case Study of Human DNA Polymerase η
Yang, W. (2014) · Biochemistry · doi:10.1021/bi500019s · Cited by 174 · see citing works
Delarue, M. H., Boulé, J.-B., Lescar, J., Expert-Bezançon, N., Jourdan, N., Sukumar, N., Rougeon, F., & Papanicolaou, C. (2002) · The EMBO Journal · doi:10.1093/emboj/21.3.427 · Cited by 173 · see citing works
Drug Targets and Molecular Mechanisms of Drug Resistance in Chronic Hepatitis B
Ghany, M. G., & Liang, T. J. (2007) · Gastroenterology · doi:10.1053/j.gastro.2007.02.039 · Cited by 172 · see citing works
Structure and Mechanism of DNA Polymerase β
Beard, W. A., & Wilson, S. H. (2014) · Biochemistry · doi:10.1021/bi500139h · Cited by 164 · see citing works
WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing
Perry, J. J. P., Yannone, S. M., Holden, L. G., Hitomi, C., Asaithamby, A., Han, S., Cooper, P. K., Chen, D. J., & Tainer, J. A. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1088 · Cited by 158 · see citing works
Structural Insights into the Origins of DNA Polymerase Fidelity
Beard, W. A., & Wilson, S. H. (2003) · Structure · doi:10.1016/s0969-2126(03)00051-0 · Cited by 157 · see citing works
DNA Structure and Aspartate 276 Influence Nucleotide Binding to Human DNA Polymerase β
Berg, B. J. V., Beard, W. A., & Wilson, S. H. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m002884200 · Cited by 154 · see citing works
Ng, K. K.-S., Cherney, M. M., Vázquez, A. L., Machín, Á., Martín-Alonso, J. M., Parra, F., & James, M. N. G. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m109261200 · Cited by 155 · see citing works
Initiation of viral RNA-dependent RNA polymerization
van Dijk, A. A., Makeyev, E. V., & Bamford, D. H. (2004) · Journal of General Virology · doi:10.1099/vir.0.19731-0 · Cited by 154 · see citing works
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP
Martin, G., Keller, W., & Doublié, S. (2000) · The EMBO Journal · doi:10.1093/emboj/19.16.4193 · Cited by 151 · see citing works
Self-citationFlorián, J., Goodman, M. F., & Warshel, A. (2003) · Journal of the American Chemical Society · doi:10.1021/ja028997o · Cited by 148 · see citing works
Mechanism of a genetic glissando*: structural biology of indel mutations
García–Díaz, M., & Kunkel, T. A. (2006) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2006.02.004 · Cited by 149 · see citing works
Structural design of a eukaryotic DNA repair polymerase: DNA polymerase β
Beard, W. A., & Wilson, S. H. (2000) · Mutation Research/DNA Repair · doi:10.1016/s0921-8777(00)00029-x · Cited by 145 · see citing works
Radhakrishnan, R., & Tamar Schlick, A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308585101 · Cited by 146 · see citing works
Dynamics of allosteric transitions in GroEL
Hyeon, C., Lorimer, G. H., & Thirumalai, D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608759103 · Cited by 145 · see citing works
Control of Hepatitis C: A Medicinal Chemistry Perspective
Gordon, C. P., & Keller, P. A. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0400101 · Cited by 143 · see citing works
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site
Hogg, M., Wallace, S. S., & Doublié, S. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600150 · Cited by 139 · see citing works
Self-citationRodriguez, A. C., Park, H.-W., Mao, C., & Beese, L. S. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3728 · Cited by 137 · see citing works
Structure and mechanism for DNA lesion recognition
Yang, W. (2007) · Cell Research · doi:10.1038/cr.2007.116 · Cited by 135 · see citing works
Joyce, C. M., Potapova, O., DeLucia, A. M., Huang, X., Basu, V. P., & Grindley, N. D. F. (2008) · Biochemistry · doi:10.1021/bi7021848 · Cited by 129 · see citing works
Yeast RNA Polymerase II at 5 Å Resolution
Fu, J., Gnatt, A. L., Bushnell, D. A., Jensen, G. J., Thompson, N. E., Burgess, R. R., David, P. R., & Kornberg, R. D. (1999) · Cell · doi:10.1016/s0092-8674(00)81514-7 · Cited by 128 · see citing works
Batra, V. K., Beard, W. A., Shock, D. D., Pedersen, L. C., & Wilson, S. H. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.02.025 · Cited by 125 · see citing works
Yeast DNA Polymerase η Utilizes an Induced-Fit Mechanism of Nucleotide Incorporation
Washington, M. T., Prakash, L., & Prakash, S. (2001) · Cell · doi:10.1016/s0092-8674(01)00613-4 · Cited by 123 · see citing works
Crystal Structure of Norwalk Virus Polymerase Reveals the Carboxyl Terminus in the Active Site Cleft
Ng, K. K.-S., Pendás-Franco, N., Rojo, J., Boga, J. A., Machín, Á., Martín-Alonso, J. M., & Parra, F. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m400584200 · Cited by 122 · see citing works
Zheng, W., Brooks, B. R., Doniach, S., & Thirumalai, D. (2005) · Structure · doi:10.1016/j.str.2005.01.017 · Cited by 121 · see citing works
Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR
Biles, B. D. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh174 · Cited by 121 · see citing works
A historical account of hoogsteen base‐pairs in duplex DNA
Nikolova, E. N., Zhou, H., Gottardo, F. L., Alvey, H. S., Kimsey, I. J., & Al‐Hashimi, H. M. (2013) · Biopolymers · doi:10.1002/bip.22334 · Cited by 120 · see citing works
Probing the active site tightness of DNA polymerase in subangstrom increments
Kim, T. W., Delaney, J. C., Essigmann, J. M., & Kool, E. T. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0505113102 · Cited by 116 · see citing works
The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus
Das, D., & Georgiadis, M. M. (2004) · Structure · doi:10.1016/j.str.2004.02.032 · Cited by 117 · see citing works
Ceramide kinase regulates growth and survival of A549 human lung adenocarcinoma cells
Mitra, P., Maceyka, M. W., Payne, S. G., Lamour, N. F., Milstien, S., Chalfant, C. E., & Spiegel, S. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.01.041 · Cited by 116 · see citing works
Structure of Yeast Poly(A) Polymerase Alone and in Complex with 3'-dATP
Bard, J., Zhelkovsky, A. M., Helmling, S., Earnest, T. N., Moore, C. L., & Bohm, A. (2000) · Science · doi:10.1126/science.289.5483.1346 · Cited by 116 · see citing works
Wu, E. Y., & Beese, L. S. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.191130 · Cited by 113 · see citing works
Structural Insight into Translesion Synthesis by DNA Pol II
Wang, F., & Yang, W. (2009) · Cell · doi:10.1016/j.cell.2009.11.043 · Cited by 112 · see citing works
Poor base stacking at DNA lesions may initiate recognition by many repair proteins
Yang, W. (2006) · DNA repair · doi:10.1016/j.dnarep.2006.02.004 · Cited by 105 · see citing works
Florián, J., Goodman, M. F., & Warshel, A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408173102 · Cited by 102 · see citing works
Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR
Kermekchiev, M. B. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg813 · Cited by 101 · see citing works
The Crystal Structure of the RNA-Dependent RNA Polymerase from Human Rhinovirus
Love, R. A., Maegley, K. A., Yu, X., Ferre, R. A., Lingardo, L., Diehl, W. C., Parge, H. E., Dragovich, P. S., & Fuhrman, S. A. (2004) · Structure · doi:10.1016/j.str.2004.05.024 · Cited by 99 · see citing works
Enzyme Tunnels and Gates As Relevant Targets in Drug Design
Marques, S. M., Daniel, L., Buryška, T., Prokop, Z., Brezovský, J., & Damborský, J. (2016) · Medicinal Research Reviews · doi:10.1002/med.21430 · Cited by 98 · see citing works
Marchand, B., & Götte, M. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m304262200 · Cited by 97 · see citing works
Hohlbein, J., Aigrain, L., Craggs, T. D., Bermek, O., Potapova, O., Shoolizadeh, P., Grindley, N. D. F., Joyce, C. M., & Kapanidis, A. N. (2013) · Nature Communications · doi:10.1038/ncomms3131 · Cited by 95 · see citing works
Portraits of a Y‐family DNA polymerase
Yang, W. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.11.047 · Cited by 92 · see citing works
Balbo, P., & Bohm, A. (2007) · Structure · doi:10.1016/j.str.2007.07.010 · Cited by 92 · see citing works
Yang, L., Beard, W. A., Wilson, S. H., Broyde, S. B., & Tamar Schlick, A. (2002) · Journal of Molecular Biology · doi:10.1006/jmbi.2002.5450 · Cited by 90 · see citing works
Structure–function studies of DNA polymerase lambda
García–Díaz, M., Bębenek, K., Gao, G., Pedersen, L. C., London, R. E., & Kunkel, T. A. (2005) · DNA repair · doi:10.1016/j.dnarep.2005.09.001 · Cited by 89 · see citing works
Variations on a theme: Eukaryotic Y-family DNA polymerases
Washington, M. T., Carlson, K. D., Freudenthal, B., & Pryor, J. M. (2009) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2009.07.004 · Cited by 87 · see citing works
Gruez, A., Selisko, B., Roberts, M. M., Bricogne, G., Bussetta, C., Jabafi, I., Coutard, B., Palma, A. M. D., Neyts, J. H., & Canard, B. (2008) · Journal of Virology · doi:10.1128/jvi.00631-08 · Cited by 87 · see citing works
Raper, A. T., Reed, A. J., & Suo, Z. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00685 · Cited by 83 · see citing works
Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution
Zhao, C., & Pyle, A. M. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3224 · Cited by 83 · see citing works
Structure of a High Fidelity DNA Polymerase Bound to a Benzo[a]pyrene Adduct That Blocks Replication
Hsu, G. W., Huang, X., Luneva, N. P., Geacintov, N. E., & Beese, L. S. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m411276200 · Cited by 82 · see citing works
Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase
Anand, V. S., & Patel, S. S. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m608180200 · Cited by 80 · see citing works
DNA Polymerase ε: A Polymerase of Unusual Size (and Complexity)
Pursell, Z. F., & Kunkel, T. A. (2008) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)00004-4 · Cited by 79 · see citing works
Beard, W. A., Shock, D. D., Yang, X., DeLauder, S. F., & Wilson, S. H. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m107286200 · Cited by 74 · see citing works
Observing Translesion Synthesis of an Aromatic Amine DNA Adduct by a High-fidelity DNA Polymerase
Hsu, G. W., Kiefer, J. R., Burnouf, D., Bécherel, O. J., Fuchs, R. P., & Beese, L. S. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m409224200 · Cited by 72 · see citing works
Inhibition of Reverse Transcription In Vivo by Elevated Manganese Ion Concentration
Bolton, E. C., Mildvan, A. S., & Boeke, J. D. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00495-1 · Cited by 72 · see citing works
Structural basis of error‐prone replication and stalling at a thymine base by human DNA polymerase ι
Kirouac, K. N., & Ling, H. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.122 · Cited by 71 · see citing works
Showalter, A. K., Lamarche, B. J., Bakhtina, M., Su, M., Tang, K., & Tsai, M. (2006) · Chemical Reviews · doi:10.1021/cr040487k · Cited by 71 · see citing works
Chinnaswamy, S., Yarbrough, I., Palaninathan, S. K., Ranjith-Kumar, C. T., Vijayaraghavan, V., Demeler, B., Lemon, S. M., Sacchettini, J. C., & Kao, C. C. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m801490200 · Cited by 68 · see citing works
Evolution of replication machines
Yao, N. Y., & O’Donnell, M. E. (2015) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2015.1125845 · Cited by 68 · see citing works
Structure and mechanism of B-family DNA polymerase ζ specialized for translesion DNA synthesis
Malik, R., Kopylov, M., Gómez-Llorente, Y., Jain, R., Johnson, R. E., Prakash, L., Prakash, S., Ubarretxena‐Belandia, I., & Aggarwal, A. K. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0476-7 · Cited by 67 · see citing works
Dutta, S., Li, Y., Johnson, D. E., Dzantiev, L., Richardson, C. C., Romano, L. J., & Ellenberger, T. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406516101 · Cited by 66 · see citing works
Self-citationDpo4 is hindered in extending a G·T mismatch by a reverse wobble
Trincão, J., Johnson, R. E., Wolfle, W. T., Escalante, C. R., Prakash, S., Prakash, L., & Aggarwal, A. K. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb755 · Cited by 63 · see citing works
Structure–Function Studies of DNA Polymerase λ
Bębenek, K., Pedersen, L. C., & Kunkel, T. A. (2014) · Biochemistry · doi:10.1021/bi4017236 · Cited by 65 · see citing works
Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S., & Aggarwal, A. K. (2006) · Structure · doi:10.1016/j.str.2006.01.010 · Cited by 65 · see citing works
The p12 Subunit of Human Polymerase δ Modulates the Rate and Fidelity of DNA Synthesis
Meng, X., Zhou, Y., Lee, E. Y. C., Lee, M., & Frick, D. N. (2010) · Biochemistry · doi:10.1021/bi100042b · Cited by 61 · see citing works
Kempeneers, V. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki695 · Cited by 60 · see citing works
Techniques used to study the DNA polymerase reaction pathway
Joyce, C. M. (2009) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2009.07.021 · Cited by 60 · see citing works
Functional Evidence for a Small and Rigid Active Site in a High Fidelity DNA Polymerase
Kim, T. W., Brieba, L. G., Ellenberger, T., & Kool, E. T. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m510744200 · Cited by 60 · see citing works
Self-citationSingle-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I
Markiewicz, R. P., Vrtis, K. B., Rueda, D., & Romano, L. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks523 · Cited by 59 · see citing works
Sesmero, E., & Thorpe, I. F. (2015) · Viruses · doi:10.3390/v7072808 · Cited by 59 · see citing works
The Mutational Specificity of the Dbh Lesion Bypass Polymerase and Its Implications
Potapova, O., Grindley, N. D. F., & Joyce, C. M. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m202607200 · Cited by 59 · see citing works
Bumps in the road: how replicative DNA polymerases see DNA damage
Hogg, M., Wallace, S. S., & Doublié, S. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.01.014 · Cited by 58 · see citing works
Self-citation
- Authors
- Doublié, S., Sawaya, M. R., & Ellenberger, T.
- Affiliations
- University of Vermont (US)
- Harvard University (US)
- Corresponding author
- Ellenberger, Tom
- Venue
- Structure
- Publisher
- Elsevier BV
- Published
- 1999-02
- Volume
- 7
- Issue
- 2
- Pages
- R31-R35
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W2036894316
- Cited by
- 314
- References
- 24
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 8 · 2023: 5 · 2022: 6 · 2021: 7 · 2020: 6 · 2019: 4 · 2018: 6 · 2017: 11 · 2016: 9 · 2015: 8 · 2014: 19 · 2013: 13 · 2012: 8
- FWCI
- 13.72
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Structure (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- polymerase active site, HIV-1 reverse transcriptase, Taq DNA polymerase, nucleotidyl transfer, conformational change, primer-template complex, rational drug design, polymerase structure
- MeSH terms
- Binding Sites, DNA-Directed DNA Polymerase, Models, Molecular, HIV-1, Protein Structure, Secondary, DNA Primers, Taq Polymerase, HIV Reverse Transcriptase
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review