-
1
-
-
0035826622
-
Insight into the catalytic mechanism of DNA polymerase β: structures of intermediate complexes
-
Arndt J.W., Gong W., Zhong X., Showalter A.K., Liu J., Dunlap C.A., Lin Z., Paxson C., Tsai M.-D., and Chan M.K. Insight into the catalytic mechanism of DNA polymerase β: structures of intermediate complexes. Biochemistry 40 (2001) 5368-5375
-
(2001)
Biochemistry
, vol.40
, pp. 5368-5375
-
-
Arndt, J.W.1
Gong, W.2
Zhong, X.3
Showalter, A.K.4
Liu, J.5
Dunlap, C.A.6
Lin, Z.7
Paxson, C.8
Tsai, M.-D.9
Chan, M.K.10
-
2
-
-
23444447967
-
Nucleotide-induced DNA polymerase active site motions accomodating a mutagenic DNA intermediate
-
Batra V.K., Beard W.A., Shock D.D., Pedersen L.C., and Wilson S.H. Nucleotide-induced DNA polymerase active site motions accomodating a mutagenic DNA intermediate. Structure (Camb) 13 (2005) 1225-1233
-
(2005)
Structure (Camb)
, vol.13
, pp. 1225-1233
-
-
Batra, V.K.1
Beard, W.A.2
Shock, D.D.3
Pedersen, L.C.4
Wilson, S.H.5
-
3
-
-
0028803178
-
Purification and domain-mapping of mammalian DNA polymerase β
-
Beard W.A., and Wilson S.H. Purification and domain-mapping of mammalian DNA polymerase β. Methods Enzymol. 262 (1995) 98-107
-
(1995)
Methods Enzymol.
, vol.262
, pp. 98-107
-
-
Beard, W.A.1
Wilson, S.H.2
-
4
-
-
0031883128
-
Structural insights into DNA polymerase β fidelity: hold tight if you want it right
-
Beard W.A., and Wilson S.H. Structural insights into DNA polymerase β fidelity: hold tight if you want it right. Chem. Biol. 5 (1998) R7-R13
-
(1998)
Chem. Biol.
, vol.5
-
-
Beard, W.A.1
Wilson, S.H.2
-
5
-
-
0034734386
-
Structural design of a eukaryotic DNA repair polymerase: DNA polymerase β
-
Beard W.A., and Wilson S.H. Structural design of a eukaryotic DNA repair polymerase: DNA polymerase β. Mutat. Res. 460 (2000) 231-244
-
(2000)
Mutat. Res.
, vol.460
, pp. 231-244
-
-
Beard, W.A.1
Wilson, S.H.2
-
6
-
-
0037566670
-
Structural insights into the origins of DNA polymerase fidelity
-
Beard W.A., and Wilson S.H. Structural insights into the origins of DNA polymerase fidelity. Structure (Camb) 11 (2003) 489-496
-
(2003)
Structure (Camb)
, vol.11
, pp. 489-496
-
-
Beard, W.A.1
Wilson, S.H.2
-
7
-
-
0037032998
-
Efficiency of correct nucleotide insertion governs DNA polymerase fidelity
-
Beard W.A., Shock D.D., Vande Berg B.J., and Wilson S.H. Efficiency of correct nucleotide insertion governs DNA polymerase fidelity. J. Biol. Chem. 277 (2002) 47393-47398
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 47393-47398
-
-
Beard, W.A.1
Shock, D.D.2
Vande Berg, B.J.3
Wilson, S.H.4
-
8
-
-
3843122085
-
Influence of DNA structure on DNA polymerase β active site function: extension of mutagenic DNA intermediates
-
Beard W.A., Shock D.D., and Wilson S.H. Influence of DNA structure on DNA polymerase β active site function: extension of mutagenic DNA intermediates. J. Biol. Chem. 279 (2004) 31921-31929
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 31921-31929
-
-
Beard, W.A.1
Shock, D.D.2
Wilson, S.H.3
-
9
-
-
0026019625
-
Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism
-
Beese L.S., and Steitz T.A. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J. 10 (1991) 25-33
-
(1991)
EMBO J.
, vol.10
, pp. 25-33
-
-
Beese, L.S.1
Steitz, T.A.2
-
11
-
-
4644259458
-
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., Doublie S., Kunkel T.A., and Ellenberger T. Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. EMBO J. 23 (2004) 3452-3461
-
(2004)
EMBO J.
, vol.23
, pp. 3452-3461
-
-
Brieba, L.G.1
Eichman, B.F.2
Kokoska, R.J.3
Doublie, S.4
Kunkel, T.A.5
Ellenberger, T.6
-
12
-
-
0032518398
-
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
-
Doublié S., Tabor S., Long A.M., Richardson C.C., and Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391 (1998) 251-258
-
(1998)
Nature
, vol.391
, pp. 251-258
-
-
Doublié, S.1
Tabor, S.2
Long, A.M.3
Richardson, C.C.4
Ellenberger, T.5
-
13
-
-
0035369086
-
Structure of the replicating complex of a pol α family DNA polymerase
-
Franklin M.C., Wang J., and Steitz T.A. Structure of the replicating complex of a pol α family DNA polymerase. Cell 105 (2001) 657-667
-
(2001)
Cell
, vol.105
, pp. 657-667
-
-
Franklin, M.C.1
Wang, J.2
Steitz, T.A.3
-
14
-
-
11444264188
-
A closed conformation for the Pol λ catalytic cycle
-
Garcia-Diaz M., Bebenek K., Krahn J.M., Kunkel T.A., and Pedersen L.C. A closed conformation for the Pol λ catalytic cycle. Nat. Struct. Mol. Biol. 12 (2005) 97-98
-
(2005)
Nat. Struct. Mol. Biol.
, vol.12
, pp. 97-98
-
-
Garcia-Diaz, M.1
Bebenek, K.2
Krahn, J.M.3
Kunkel, T.A.4
Pedersen, L.C.5
-
15
-
-
0035094475
-
Geometry of metal-ligand interactions in proteins
-
Harding M.M. Geometry of metal-ligand interactions in proteins. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 401-411
-
(2001)
Acta Crystallogr. D Biol. Crystallogr.
, vol.57
, pp. 401-411
-
-
Harding, M.M.1
-
16
-
-
0036014793
-
Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium
-
Harding M.M. Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. Acta Crystallogr. D Biol. Crystallogr. 58 (2002) 872-874
-
(2002)
Acta Crystallogr. D Biol. Crystallogr.
, vol.58
, pp. 872-874
-
-
Harding, M.M.1
-
17
-
-
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. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282 (1998) 1669-1675
-
(1998)
Science
, vol.282
, pp. 1669-1675
-
-
Huang, H.1
Chopra, R.2
Verdine, G.L.3
Harrison, S.C.4
-
18
-
-
0037388383
-
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
-
Johnson S.J., Taylor J.S., and Beese L.S. Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc. Natl. Acad. Sci. USA 100 (2003) 3895-3900
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3895-3900
-
-
Johnson, S.J.1
Taylor, J.S.2
Beese, L.S.3
-
19
-
-
8544278025
-
DNA polymerase fidelity: kinetics, structure, and checkpoints
-
Joyce C.M., and Benkovic S.J. DNA polymerase fidelity: kinetics, structure, and checkpoints. Biochemistry 43 (2004) 14317-14324
-
(2004)
Biochemistry
, vol.43
, pp. 14317-14324
-
-
Joyce, C.M.1
Benkovic, S.J.2
-
20
-
-
0037227566
-
Structure of DNA polymerase β with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential
-
Krahn J.M., Beard W.A., Miller H., Grollman A.P., and Wilson S.H. Structure of DNA polymerase β with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure (Camb) 11 (2003) 121-127
-
(2003)
Structure (Camb)
, vol.11
, pp. 121-127
-
-
Krahn, J.M.1
Beard, W.A.2
Miller, H.3
Grollman, A.P.4
Wilson, S.H.5
-
21
-
-
4644258145
-
Structural insights into DNA polymerase deterrents for misincorportion support an induced-fit mechanism for fidelity
-
Krahn J.M., Beard W.A., and Wilson S.H. Structural insights into DNA polymerase deterrents for misincorportion support an induced-fit mechanism for fidelity. Structure (Camb) 12 (2004) 1823-1832
-
(2004)
Structure (Camb)
, vol.12
, pp. 1823-1832
-
-
Krahn, J.M.1
Beard, W.A.2
Wilson, S.H.3
-
22
-
-
0026244229
-
MOLSCRIPT: a program to produce both detailed and schematic plots of proteins
-
Kraulis P. MOLSCRIPT: a program to produce both detailed and schematic plots of proteins. J. Appl. Crystallogr. 24 (1991) 946-950
-
(1991)
J. Appl. Crystallogr.
, vol.24
, pp. 946-950
-
-
Kraulis, P.1
-
23
-
-
0032535528
-
Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation
-
Li Y., Korolev S., and Waksman G. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J. 17 (1998) 7514-7525
-
(1998)
EMBO J.
, vol.17
, pp. 7514-7525
-
-
Li, Y.1
Korolev, S.2
Waksman, G.3
-
24
-
-
0033578332
-
Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation
-
Li Y., Mitaxov V., and Waksman G. Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. Proc. Natl. Acad. Sci. USA 96 (1999) 9491-9496
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 9491-9496
-
-
Li, Y.1
Mitaxov, V.2
Waksman, G.3
-
25
-
-
3543002207
-
Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7
-
Li Y., Dutta S., Doublié S., Bdour H.M., Taylor J.-S., and Ellenberger T. Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. Nat. Struct. Mol. Biol. 11 (2004) 784-790
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 784-790
-
-
Li, Y.1
Dutta, S.2
Doublié, S.3
Bdour, H.M.4
Taylor, J.-S.5
Ellenberger, T.6
-
26
-
-
0035812849
-
Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication
-
Ling H., Boudsocq F., Woodgate R., and Yang W. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107 (2001) 91-102
-
(2001)
Cell
, vol.107
, pp. 91-102
-
-
Ling, H.1
Boudsocq, F.2
Woodgate, R.3
Yang, W.4
-
27
-
-
0037441653
-
Structure validation by Cα geometry: φ{symbol},ψ and Cß deviation
-
Lovell S.C., Davis I.W., Arendall III W.B., de Bakker P.I.W., Word J.M., Prisant M.G., Richardson J.S., and Richardson D.C. Structure validation by Cα geometry: φ{symbol},ψ and Cß deviation. Proteins 50 (2003) 437-450
-
(2003)
Proteins
, vol.50
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall III, W.B.3
de Bakker, P.I.W.4
Word, J.M.5
Prisant, M.G.6
Richardson, J.S.7
Richardson, D.C.8
-
28
-
-
0030815133
-
Raster3D: photorealistic molecular graphics
-
Merritt E.A., and Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524
-
(1997)
Methods Enzymol.
, vol.277
, pp. 505-524
-
-
Merritt, E.A.1
Bacon, D.J.2
-
29
-
-
0030724727
-
Mechanisms of signaling and related enzymes
-
Mildvan A.S. Mechanisms of signaling and related enzymes. Proteins 29 (1997) 401-416
-
(1997)
Proteins
, vol.29
, pp. 401-416
-
-
Mildvan, A.S.1
-
31
-
-
25844440534
-
Rev1 employs a novel mechanism of DNA synthesis using a protein template
-
Nair D.T., Johnson R.E., Prakash L., Prakash S., and Aggarwal A.K. Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science 309 (2005) 2219-2222
-
(2005)
Science
, vol.309
, pp. 2219-2222
-
-
Nair, D.T.1
Johnson, R.E.2
Prakash, L.3
Prakash, S.4
Aggarwal, A.K.5
-
32
-
-
26444528004
-
Human DNA polymerase ι incorporates dCTP opposite template G via a G.C+ Hoogsteen base pair
-
Nair D.T., Johnson R.E., Prakash L., Prakash S., and Aggarwal A.K. Human DNA polymerase ι incorporates dCTP opposite template G via a G.C+ Hoogsteen base pair. Structure (Camb) 13 (2005) 1569-1577
-
(2005)
Structure (Camb)
, vol.13
, pp. 1569-1577
-
-
Nair, D.T.1
Johnson, R.E.2
Prakash, L.3
Prakash, S.4
Aggarwal, A.K.5
-
33
-
-
0031059866
-
Processsing of X-ray diffraction data collected in oscillation mode
-
Otwinowski Z., and Minor W. Processsing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
34
-
-
0028566215
-
Polymerase structures and mechanism
-
Pelletier H. Polymerase structures and mechanism. Science 266 (1994) 2025-2026
-
(1994)
Science
, vol.266
, pp. 2025-2026
-
-
Pelletier, H.1
-
35
-
-
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. Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science 264 (1994) 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
-
36
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25 (2004) 1605-1612
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
37
-
-
0026713678
-
Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli
-
Polesky A.H., Dahlberg M.E., Benkovic S.J., Grindley N.D., and Joyce C.M. Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli. J. Biol. Chem. 267 (1992) 8417-8428
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 8417-8428
-
-
Polesky, A.H.1
Dahlberg, M.E.2
Benkovic, S.J.3
Grindley, N.D.4
Joyce, C.M.5
-
38
-
-
27844562272
-
Structural insight into the DNA polymertase β deoxyribose phosphate lyase mechanism
-
Prasad R., Batra V.K., Yang X.-P., Krahn J.M., Pedersen L.C., Beard W.A., and Wilson S.H. Structural insight into the DNA polymertase β deoxyribose phosphate lyase mechanism. DNA Repair (Amst.) 4 (2005) 1347-1357
-
(2005)
DNA Repair (Amst.)
, vol.4
, pp. 1347-1357
-
-
Prasad, R.1
Batra, V.K.2
Yang, X.-P.3
Krahn, J.M.4
Pedersen, L.C.5
Beard, W.A.6
Wilson, S.H.7
-
39
-
-
0028136070
-
Crystal structure of rat DNA polymerase β: evidence for a common polymerase mechanism
-
Sawaya M.R., Pelletier H., Kumar A., Wilson S.H., and Kraut J. Crystal structure of rat DNA polymerase β: evidence for a common polymerase mechanism. Science 264 (1994) 1930-1935
-
(1994)
Science
, vol.264
, pp. 1930-1935
-
-
Sawaya, M.R.1
Pelletier, H.2
Kumar, A.3
Wilson, S.H.4
Kraut, J.5
-
40
-
-
0030930760
-
Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: evidence for an induced fit mechanism
-
Sawaya M.R., Prasad P., Wilson S.H., Kraut J., and Pelletier H. Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry 36 (1997) 11205-11215
-
(1997)
Biochemistry
, vol.36
, pp. 11205-11215
-
-
Sawaya, M.R.1
Prasad, P.2
Wilson, S.H.3
Kraut, J.4
Pelletier, H.5
-
41
-
-
0017173641
-
Infidelity of DNA synthesis in vitro: screening for potential metal mutagens or carcinogens
-
Sirover M.A., and Loeb L.A. Infidelity of DNA synthesis in vitro: screening for potential metal mutagens or carcinogens. Science 194 (1976) 1434-1436
-
(1976)
Science
, vol.194
, pp. 1434-1436
-
-
Sirover, M.A.1
Loeb, L.A.2
-
42
-
-
0034659935
-
The lyase activity of the DNA repair protein β-polymerase protects from DNA-damage-induced cytotoxicity
-
Sobol R.W., Prasad R., Evenski A., Baker A., Yang X.P., Horton J.K., and Wilson S.H. The lyase activity of the DNA repair protein β-polymerase protects from DNA-damage-induced cytotoxicity. Nature 405 (2000) 807-810
-
(2000)
Nature
, vol.405
, pp. 807-810
-
-
Sobol, R.W.1
Prasad, R.2
Evenski, A.3
Baker, A.4
Yang, X.P.5
Horton, J.K.6
Wilson, S.H.7
-
43
-
-
0033581011
-
DNA polymerases: structural diversity and common mechanisms
-
Steitz T.A. DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274 (1999) 17395-17398
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 17395-17398
-
-
Steitz, T.A.1
-
44
-
-
0027819734
-
Two DNA polymerases: HIV reverse transcriptase and the Klenow fragment of Escherichia coli DNA polymerase I
-
Steitz T.A., Smerdon S., Jäger J., Wang J., Kohlstaedt L.A., Friedman J.M., Beese L.S., and Rice P.A. Two DNA polymerases: HIV reverse transcriptase and the Klenow fragment of Escherichia coli DNA polymerase I. Cold Spring Harb. Symp. Quant. Biol. 58 (1993) 495-504
-
(1993)
Cold Spring Harb. Symp. Quant. Biol.
, vol.58
, pp. 495-504
-
-
Steitz, T.A.1
Smerdon, S.2
Jäger, J.3
Wang, J.4
Kohlstaedt, L.A.5
Friedman, J.M.6
Beese, L.S.7
Rice, P.A.8
-
45
-
-
0028606031
-
A unified polymerase mechanism for nonhomologous DNA and RNA polymerases
-
Steitz T.A., Smerdon S.J., Jager J., and Joyce C.M. A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science 266 (1994) 2022-2025
-
(1994)
Science
, vol.266
, pp. 2022-2025
-
-
Steitz, T.A.1
Smerdon, S.J.2
Jager, J.3
Joyce, C.M.4
-
46
-
-
25144479978
-
DNA polymerases: Hoogsteen base-pairing in DNA replication?
-
Wang J. DNA polymerases: Hoogsteen base-pairing in DNA replication?. Nature 437 (2005) E6-E7
-
(2005)
Nature
, vol.437
-
-
Wang, J.1
-
47
-
-
0036295231
-
Polymerase β simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se
-
Yang L., Beard W.A., Wilson S.H., Broyde S., and Schlick T. Polymerase β simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. J. Mol. Biol. 317 (2002) 679-699
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 679-699
-
-
Yang, L.1
Beard, W.A.2
Wilson, S.H.3
Broyde, S.4
Schlick, T.5
-
48
-
-
3142702966
-
Critical role of magnesium ions in DNA polymerase β's closing and active site assembly
-
Yang L., Arora K., Beard W.A., Wilson S.H., and Schlick T. Critical role of magnesium ions in DNA polymerase β's closing and active site assembly. J. Am. Chem. Soc. 126 (2004) 8441-8453
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 8441-8453
-
-
Yang, L.1
Arora, K.2
Beard, W.A.3
Wilson, S.H.4
Schlick, T.5
|