-
1
-
-
0025783442
-
Fidelity mechanisms inDNA replication
-
Echols, H., and Goodman, M. F. (1991) Fidelity mechanisms inDNA replication. Annu. Rev. Biochem. 60, 477-511.
-
(1991)
Annu. Rev. Biochem.
, vol.60
, pp. 477-511
-
-
Echols, H.1
Goodman, M.F.2
-
2
-
-
0028206048
-
Function and structure relationships in DNA polymerases
-
Joyce, C. M., and Steitz, T. A. (1994) Function and structure relationship in DNA polymerases. Annu. Rev. Biochem. 63, 777-822. (Pubitemid 24218649)
-
(1994)
Annual Review of Biochemistry
, vol.63
, pp. 777-822
-
-
Joyce, C.M.1
Steitz, T.A.2
-
3
-
-
77949570420
-
The kinetic and chemical mechanism of highfidelity DNA polymerases
-
Johnson, K. A. (2010) The kinetic and chemical mechanism of highfidelity DNA polymerases. Biochim. Biophys. Acta 1804, 1041-1048.
-
(2010)
Biochim. Biophys. Acta
, vol.1804
, pp. 1041-1048
-
-
Johnson, K.A.1
-
4
-
-
0027217643
-
Compilation, alignment, and phlogenetic relationships ofDNApolymerases
-
Braithwaite, D. K., and Ito, J. (1993) Compilation, alignment, and phlogenetic relationships ofDNApolymerases. Nucleic Acids Res. 21, 787-802.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 787-802
-
-
Braithwaite, D.K.1
Ito, J.2
-
5
-
-
0031587827
-
Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69
-
Wang, J., Sattar, A. K., Wang, C. C., Karam, J. D., Konigsberg, W. H., and Steitz, T. A. (1997) Crystal structure of a pol R family replication DNA polymerase from bacteriophage RB69. Cell 89, 1087-1099. (Pubitemid 127678742)
-
(1997)
Cell
, vol.89
, Issue.7
, pp. 1087-1099
-
-
Wang, J.1
Sattar, A.K.M.A.2
Wang, C.C.3
Karam, J.D.4
Konigsberg, W.H.5
Steitz, T.A.6
-
6
-
-
0035369086
-
Structure of the replicating complex of a pol α family DNA polymerase
-
DOI 10.1016/S0092-8674(01)00367-1
-
Franklin, M. C., Wang, J., and Steitz, T. A. (2001) Structure of the replicating complex of a pol R familyDNApolymerase. Cell 105, 657-667. (Pubitemid 32524118)
-
(2001)
Cell
, vol.105
, Issue.5
, pp. 657-667
-
-
Franklin, M.C.1
Wang, J.2
Steitz, T.A.3
-
7
-
-
33747462891
-
A new paradigm for DNA polymerase specificity
-
Tsai, Y. C., and Johnson, K. A. (2006) A new paradigm for DNA polymerase specificity. Biochemistry 45, 9675-9685.
-
(2006)
Biochemistry
, vol.45
, pp. 9675-9685
-
-
Tsai, Y.C.1
Johnson, K.A.2
-
8
-
-
0024819551
-
Oligonucleotide structure: A decade of results from single crystal X-ray diffraction studies
-
Kennard, O., and Hunter, W. N. (1989) Oligonucleotide structure: A decade of results from single crystal X-ray diffraction studies. Q. Rev. Biophys. 22, 327-379. (Pubitemid 20040753)
-
(1989)
Quarterly Reviews of Biophysics
, vol.22
, Issue.3
, pp. 327-379
-
-
Kennard, O.1
Hunter, W.N.2
-
9
-
-
0027247430
-
Oligonucleotide x-ray structures in the study of conformation and interactions of nucleic acids
-
Kennard, O., and Salisbury, S. A. (1993) Oligonucleotide X-ray structures in the study of conformation and interactions of nucleic acids. J. Biol. Chem. 268, 10701-10704. (Pubitemid 23162241)
-
(1993)
Journal of Biological Chemistry
, vol.268
, Issue.15
, pp. 10701-10704
-
-
Kennard, O.1
Salisbury, S.A.2
-
10
-
-
0030592095
-
Structure of Taq polymerase with DNA at the polymerase active site
-
DOI 10.1038/382278a0
-
Eom, S. H., Wang, J., and Steitz, T. A. (1996) Structure of Taq polymerase withDNAat the polymerase active site. Nature 382, 278-281 (Pubitemid 26255301)
-
(1996)
Nature
, vol.382
, Issue.6588
, pp. 278-281
-
-
Soo Hyun Eom1
Wang, J.2
Steitz, T.A.3
-
11
-
-
1642588255
-
Structures of mismatch replication errors observed in a DNA polymerase
-
DOI 10.1016/S0092-8674(04)00252-1, PII S0092867404002521
-
Johnson, S. J., and Beese, L. S. (2004) Structures of mismatch replication errors observed in a DNA polymerase. Cell 116, 803-816. (Pubitemid 38410726)
-
(2004)
Cell
, vol.116
, Issue.6
, pp. 803-816
-
-
Johnson, S.J.1
Beese, L.S.2
-
12
-
-
0028049441
-
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., and Kraut, J. (1994) Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science 264, 1891-1903.
-
(1994)
Science
, vol.264
, pp. 1891-1903
-
-
Pelletier, H.1
Sawaya, M.R.2
Kumar, A.3
Wilson, S.H.4
Kraut, J.5
-
13
-
-
0032518398
-
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
-
DOI 10.1038/34593
-
Doublie, S., Tabor, S., Long, A. M., Richardson, C. C., and Ellenberger, T. (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391, 251-258. (Pubitemid 28099004)
-
(1998)
Nature
, vol.391
, Issue.6664
, pp. 251-258
-
-
Doublie, S.1
Tabor, S.2
Long, A.M.3
Richardson, C.C.4
Ellenberger, T.5
-
14
-
-
0032573488
-
Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance
-
Huang, H., Chopra, R., Verdine, G. L., and Harrison, S. C. (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance. Science 282, 1669-1675. (Pubitemid 28549275)
-
(1998)
Science
, vol.282
, Issue.5394
, pp. 1669-1675
-
-
Huang, H.1
Chopra, R.2
Verdine, G.L.3
Harrison, S.C.4
-
15
-
-
0030930760
-
Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
-
DOI 10.1021/bi9703812
-
Sawaya, M. R., Prasad, R., Wilson, S. H., Kraut, J., and Pelletier, H. (1997) Crystal structures of human DNA polymerase β complexes with gapped and nicked DNA: Evidence for an induced fit mechanism. Biochemistry 36, 11205-11215. (Pubitemid 27398440)
-
(1997)
Biochemistry
, vol.36
, Issue.37
, pp. 11205-11215
-
-
Sawaya, M.R.1
Prasad, R.2
Wilson, S.H.3
Kraut, J.4
Pelletier, H.5
-
16
-
-
34547175132
-
Structures of φ29 DNA polymerase complexed with substrate: The mechanism of tanslocation in B-family polymerases
-
Berman, A. J., Kamtekar, S., Goodman, J. L., Lazaro, J. M., deVega, M., Blanco, L., Salas, M., and Steitz, T. A. (2007) Structures of φ29 DNA polymerase complexed with substrate: The mechanism of tanslocation in B-family polymerases. EMBO J. 26, 3496-3505.
-
(2007)
EMBO J.
, vol.26
, pp. 3496-3505
-
-
Berman, A.J.1
Kamtekar, S.2
Goodman, J.L.3
Lazaro, J.M.4
Devega, M.5
Blanco, L.6
Salas, M.7
Steitz, T.A.8
-
17
-
-
69949128706
-
Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase δ
-
Swan, M. S., Johnson, R. E., Prakash, L., Prakash, S., and Aggarwal, A. K. (2007) Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase δ. Nat. Struct. Mol. Biol. 16, 979-986.
-
(2007)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 979-986
-
-
Swan, M.S.1
Johnson, R.E.2
Prakash, L.3
Prakash, S.4
Aggarwal, A.K.5
-
18
-
-
33144478306
-
The L561A substitution in the nascent base-pair binding pocket of RB69 DNA polymerase reduces base discrimination
-
DOI 10.1021/bi052099y
-
Zhang, H., Rhee, C., Bebenek, A., Drake, J. W., Wang, J., and Konigsberg, W. (2006) The L561A substitution in the nascent basepair binding pocket of RB69 DNA polymerase reduces base discrimination. Biochemistry 45, 2211-2220. (Pubitemid 43271320)
-
(2006)
Biochemistry
, vol.45
, Issue.7
, pp. 2211-2220
-
-
Zhang, H.1
Rhee, C.2
Bebenek, A.3
Drake, J.W.4
Wang, J.5
Konigsberg, W.6
-
19
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
DOI 10.1016/S0076-6879(97)76066-X
-
Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology (Carter, C. W., and Sweet, R. M., Eds.) pp 307-326, Academic Press, San Diego. (Pubitemid 27085611)
-
(1997)
Methods in Enzymology
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
20
-
-
34447508216
-
Phaser crystallographic software
-
McCoy, A. J., Grosse-Kunstev, R. W., Adams, P. D., Win, L. C., Storoni, L. C., and Read, R. J. (2007) Phaser crystallographic software. J. Appl. Crystallogr. 40, 458-674.
-
(2007)
J. Appl. Crystallogr.
, vol.40
, pp. 458-674
-
-
McCoy, A.J.1
Grosse-Kunstev, R.W.2
Adams, P.D.3
Win, L.C.4
Storoni, L.C.5
Read, R.J.6
-
22
-
-
0030924992
-
Refinement of macromolecular structures by the maximum-likelihood method
-
DOI 10.1107/S0907444996012255
-
Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240-255. (Pubitemid 27235885)
-
(1997)
Acta Crystallographica Section D: Biological Crystallography
, vol.53
, Issue.3
, pp. 240-255
-
-
Murshudov, G.N.1
Vagin, A.A.2
Dodson, E.J.3
-
23
-
-
0037418665
-
14 at 2.0 Å resolution
-
DOI 10.1016/S0022-2836(03)00184-0
-
Wang, J., and Boisvert, D. C. (2003) Structural basis for GroELassisted protein folding from the crystal structure of (GroELKMgATP) 14 at 2.0 Å resolution. J. Mol. Biol. 327, 843-855. (Pubitemid 36315923)
-
(2003)
Journal of Molecular Biology
, vol.327
, Issue.4
, pp. 843-855
-
-
Wang, J.1
Boisvert, D.C.2
-
25
-
-
0025280401
-
Structural studies of protein-nucleic acid interaction: The sources of sequence-specific binding
-
Steitz, T. A. (1990) Structural studies of protein-nucleic acid interaction: The sources of sequence-specific binding. Q. Rev. Biophys. 23, 205-280.
-
(1990)
Q. Rev. Biophys.
, vol.23
, pp. 205-280
-
-
Steitz, T.A.1
-
26
-
-
0024294634
-
Crystal structure of trp repressor/operator complex at atomic resolution
-
Otwinowski, Z., Schevitz, R. W., Zhang, R. G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F., and Sigler, P. B. (1988) Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335, 321-329.
-
(1988)
Nature
, vol.335
, pp. 321-329
-
-
Otwinowski, Z.1
Schevitz, R.W.2
Zhang, R.G.3
Lawson, C.L.4
Joachimiak, A.5
Marmorstein, R.Q.6
Luisi, B.F.7
Sigler, P.B.8
-
27
-
-
0035979146
-
The Cα - H---O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions
-
DOI 10.1073/pnas.161280798
-
Senes, A., Ubarretxena-Belandia, I., and Engelman, D.M. (2001) The CR-H 3 3 3O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions. Proc. Natl. Acad. Sci. U.S.A. 98, 9056-9061. (Pubitemid 32743868)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.16
, pp. 9056-9061
-
-
Senes, A.1
Ubarretxena-Belandia, I.2
Engelman, D.M.3
-
28
-
-
0016709657
-
Quantitative determination of the conformation of ATP in aqueous solution using the lanthanide cations as nuclear-magneticresonance probes
-
Tanswell, P., Thornton, J. M., Korda, A. V., and Williams, R. J. P. (1975) Quantitative determination of the conformation of ATP in aqueous solution using the lanthanide cations as nuclear-magneticresonance probes. Eur. J. Biochem. 57, 135-145.
-
(1975)
Eur. J. Biochem.
, vol.57
, pp. 135-145
-
-
Tanswell, P.1
Thornton, J.M.2
Korda, A.V.3
Williams, R.J.P.4
-
30
-
-
67651218926
-
RB69 DNA polymerase mutants with expanded nascent base-pair-binding pockets are highly efficient but reduced base selectivity
-
Zhang, H., Beckman, J., Wang, J., and Konigsberg, W. (2009) RB69 DNA polymerase mutants with expanded nascent base-pair-binding pockets are highly efficient but reduced base selectivity. Biochemistry 48, 6940-6950.
-
(2009)
Biochemistry
, vol.48
, pp. 6940-6950
-
-
Zhang, H.1
Beckman, J.2
Wang, J.3
Konigsberg, W.4
-
31
-
-
0037176870
-
Correlation of the kinetics of finger domain mutants in RB69 DNA polymerase with its structure
-
DOI 10.1021/bi0119924
-
Yang, G., Franklin, M., Li., J., Lin, T. C., and Konigsberg, W. (2002) Correlation of the kinetics of finger domain mutants in RB69 DNA polymerase with its structure. Biochemistry 41, 2526-2534. (Pubitemid 34168921)
-
(2002)
Biochemistry
, vol.41
, Issue.8
, pp. 2526-2534
-
-
Yang, G.1
Franklin, M.2
Li, J.3
Lin, T.-C.4
Konigsberg, W.5
-
32
-
-
23044492225
-
Motions of the fingers subdomain of Klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases
-
DOI 10.1016/j.molcel.2005.06.032, PII S1097276505014358
-
Rothwell, P. J., Mitaksov, V., and Waksman, G. (2005) Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases. Mol. Cell 19, 345-355. (Pubitemid 41074890)
-
(2005)
Molecular Cell
, vol.19
, Issue.3
, pp. 345-355
-
-
Rothwell, P.J.1
Mitaksov, V.2
Waksman, G.3
-
33
-
-
0028033533
-
The slow dissociation of the T4 DNA polymerase holoenzyme when stalled by nucleotide omission. An indication of a highly processive enzyme
-
Hacker, K. J., and Alberts, B. M. (1994) The slow dissociation of the T4 DNA polymerase holoenzyme when stalled by nucleotide omission. An indication of a highly processive enzyme. J. Biol.Chem. 269, 24209-24220.
-
(1994)
J. Biol.Chem.
, vol.269
, pp. 24209-24220
-
-
Hacker, K.J.1
Alberts, B.M.2
-
34
-
-
0028147234
-
The rapid dissociation of the T4 DNA polymerase holoenzyme when stopped by a DNA hairping helix. A model for polymerase release following the termination of each Okazaki fragment
-
Hacker, K. J., and Alberts, B. M. (1994) The rapid dissociation of the T4 DNA polymerase holoenzyme when stopped by a DNA hairping helix. A model for polymerase release following the termination of each Okazaki fragment. J. Biol. Chem. 269, 24221-24228.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 24221-24228
-
-
Hacker, K.J.1
Alberts, B.M.2
-
35
-
-
0343471361
-
Dissociation of bacteriophage T4 DNA polymerase and its processivity clamp after completion of okazaki fragment synthesis
-
DOI 10.1021/bi971423p
-
Carver, T. E., Jr., Sexton, D. J., and Benkovic, S. J. (1997) Dissociation of bacteriophage T4 DNA polymerase and its processivity clamp after completion of Okazaki fragment synthesis. Biochemistry 36, 14409-14417. (Pubitemid 27509933)
-
(1997)
Biochemistry
, vol.36
, Issue.47
, pp. 14409-14417
-
-
Carver Jr., T.E.1
Sexton, D.J.2
Benkovic, S.J.3
-
36
-
-
30744446944
-
The control mechanism for lagging strand polymerase recycling during bacteriophage T4 DNA replication
-
DOI 10.1016/j.molcel.2005.11.029, PII S1097276505018447
-
Yang, J., Nelson, S. W., and Benkovic, S. J. (2006) The control mechanism for lagging strand polymerase recycling during bacteriophage T4 DNA replication. Mol. Cell 21, 153-164. (Pubitemid 43099932)
-
(2006)
Molecular Cell
, vol.21
, Issue.2
, pp. 153-164
-
-
Yang, J.1
Nelson, S.W.2
Benkovic, S.J.3
-
37
-
-
0033616725
-
Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius
-
DOI 10.1073/pnas.96.7.3600
-
Hopfner, K. P., Eichinger, A., Engh, R. A., Laue, F., Ankenbauer, W., Huber, R., and Angerer, B. (1999) Crystal structure of a thermostable type BDNApolymerase from Thermococcus gorgonarius. Proc. Natl. Acad. Sci. U.S.A. 96, 3600-3605. (Pubitemid 29168956)
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, Issue.7
, pp. 3600-3605
-
-
Hopfner, K.-P.1
Eichinger, A.2
Engh, R.A.3
Laue, F.4
Ankenbauer, W.5
Huber, R.6
Angerer, B.7
-
38
-
-
0033570179
-
Crystal structure of an archaebacterial DNA polymerase
-
DOI 10.1016/S0969-2126(00)80053-2
-
Zhao, Y., Jeruzalmi, D., Moarefi, I., Leighton, L., Lasken, R., and Kuriyan, J. (1999) Crystal structure of an archaebacterial DNA polymerase. Structure 7, 1189-1199. (Pubitemid 29482981)
-
(1999)
Structure
, vol.7
, Issue.10
, pp. 1189-1199
-
-
Zhao, Y.1
Jeruzalmi, D.2
Moarefi, I.3
Leighton, L.4
Lasken, R.5
Kuriyan, J.6
-
39
-
-
0034595517
-
Crystal structure of pol R family DNA polymerase from the hyperthermophilic archaeon thermococcus sp. 9-N-7
-
Rodriguez, A. C., Park, H. K., Mao, C., and Beese, L. (2000) Crystal structure of pol R family DNA polymerase from the hyperthermophilic archaeon thermococcus sp. 9-N-7. J. Mol. Biol. 299, 447-462.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 447-462
-
-
Rodriguez, A.C.1
Park, H.K.2
Mao, C.3
Beese, L.4
-
40
-
-
0035936690
-
Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1
-
DOI 10.1006/jmbi.2000.4403
-
Hashimoto, H., Nishioka, M., Fujiwara, S., Takagi, M., Imanaka, T., Inoue, T., and Kai, Y. (2001) Crystal structure of DNA polymerase fro hyperthermophilic archaeon Pyrococcus kodakaranesis KOD1. J. Mol. Biol. 306, 469-477. (Pubitemid 33027715)
-
(2001)
Journal of Molecular Biology
, vol.306
, Issue.3
, pp. 469-477
-
-
Hashimoto, H.1
Nishioka, M.2
Fujiwara, S.3
Takagi, M.4
Imanaka, T.5
Inoue, T.6
Kai, Y.7
-
41
-
-
0036894880
-
Structural basis for uracil recognition by archaeal family B DNA polymerases
-
DOI 10.1038/nsb867
-
Fogg, M. J., Pearl, L. H., and Connolly, B. A. (2002) Structural basis for uracil recognition by archaeal family B DNA polymerase. Nat. Struct. Biol. 9, 922-927. (Pubitemid 35417061)
-
(2002)
Nature Structural Biology
, vol.9
, Issue.12
, pp. 922-927
-
-
Fogg, M.J.1
Pearl, L.H.2
Connolly, B.A.3
-
42
-
-
7944222972
-
Insights into DNA replication: The crystal structure of DNA polymerase B1 from the archaeon Sulfolobus solfataricus
-
DOI 10.1016/j.str.2004.09.007, PII S0969212604003338
-
Savino, C., Federici, L., Johnson, K. A., Vallone, B., Nastopoulos, V., Rossi, M., Pisani, F. M., and Tsernoglou, D. (2004) Insights into DNA replication: The crystal structure of DNA polymerase B1 from the archeaon Sulfolobus solfataricus. Structure 12, 2001-2008. (Pubitemid 39469397)
-
(2004)
Structure
, vol.12
, Issue.11
, pp. 2001-2008
-
-
Savino, C.1
Federici, L.2
Johnson, K.A.3
Vallone, B.4
Nastopoulos, V.5
Rossi, M.6
Pisani, F.M.7
Tsernoglou, D.8
-
43
-
-
47849125401
-
Uracil recognition in archaeal DNA polymerase captured by X-ray crystallography
-
Firbank, S. J., Wardle, J., Heslop, P., Lewis, R. J., and Connolly, B.A. (2008) Uracil recognition in archaeal DNA polymerase captured by X-ray crystallography. J. Mol. Biol. 381, 529-539.
-
(2008)
J. Mol. Biol.
, vol.381
, pp. 529-539
-
-
Firbank, S.J.1
Wardle, J.2
Heslop, P.3
Lewis, R.J.4
Connolly, B.A.5
-
44
-
-
0035812849
-
Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication
-
DOI 10.1016/S0092-8674(01)00515-3
-
Ling, H., Boudsocq, F., Woodgate, R., and Yang, W. (2001) Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication. Cell 107, 91-102. (Pubitemid 32972040)
-
(2001)
Cell
, vol.107
, Issue.1
, pp. 91-102
-
-
Ling, H.1
Boudsocq, F.2
Woodgate, R.3
Yang, W.4
|