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1
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0030861915
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DNA glycosylases in the base excision repair of DNA
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An excellent and comprehensive review on DNA glycosylases, focusing on their biochemistry and structure.
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Krokan HE, Standal R, Slupphaug G DNA glycosylases in the base excision repair of DNA. Biochem J. 325:1997;1-16. An excellent and comprehensive review on DNA glycosylases, focusing on their biochemistry and structure.
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(1997)
Biochem J
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Krokan, H.E.1
Standal, R.2
Slupphaug, G.3
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2
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0031025997
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Defective transcription-coupled repair of oxidative damage in Cockayne syndrome patients from XP group G
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The authors report the breakthrough discovery that the transcription-coupled repair of oxidative damage is executed by BER and that this repair requires an XPG function that is distinct from its nucleotide excision repair (NER) activity. Thus, XPG interactions influence both the BER and the NER pathways.
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Cooper PK, Nouspikel T, Clarkson SG, Leadon SA Defective transcription-coupled repair of oxidative damage in Cockayne syndrome patients from XP group G. Science. 275:1997;990-993. The authors report the breakthrough discovery that the transcription-coupled repair of oxidative damage is executed by BER and that this repair requires an XPG function that is distinct from its nucleotide excision repair (NER) activity. Thus, XPG interactions influence both the BER and the NER pathways.
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(1997)
Science
, vol.275
, pp. 990-993
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Cooper, P.K.1
Nouspikel, T.2
Clarkson, S.G.3
Leadon, S.A.4
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3
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0032516831
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Mammalian abasic site base excision repair: Identification of the reaction sequence and rate-determining steps
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The reconstitution of AP site repair in vitro using APE, Polβ and DNA ligase I shows that Polβ synthesizes a nucleotide replacement for the damaged base before removing the dRP moiety. Furthermore, this dRPase activity is rate limiting among these enzymes in vitro
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Srivastava DK, Vande Berg BJ, Prasad R, Molina JT, Beard WA, Tomkinson AE, Wilson SH Mammalian abasic site base excision repair: identification of the reaction sequence and rate-determining steps. J Biol Chem. 273:1998;21203-21209. The reconstitution of AP site repair in vitro using APE, Polβ and DNA ligase I shows that Polβ synthesizes a nucleotide replacement for the damaged base before removing the dRP moiety. Furthermore, this dRPase activity is rate limiting among these enzymes in vitro.
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(1998)
J Biol Chem
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Srivastava, D.K.1
Vande Berg, B.J.2
Prasad, R.3
Molina, J.T.4
Beard, W.A.5
Tomkinson, A.E.6
Wilson, S.H.7
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4
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0032502675
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Involvement of flap endonuclease 1 in base excision DNA repair
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Kim K, Biade S, Matsumoto Y Involvement of flap endonuclease 1 in base excision DNA repair. J Biol Chem. 273:1998;8842-8848.
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J Biol Chem
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Kim, K.1
Biade, S.2
Matsumoto, Y.3
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5
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0030957997
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Second pathway for completion of human DNA base excision-repair: Reconstitution with purified proteins and requirement for DNase IV (FEN1)
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The long-patch BER pathway was reconstituted in vitro using Polβ or Polδ, FEN-1, PCNA and DNA ligase I. This FEN-1-dependent pathway was essential for the repair of reduced AP sites and is required for the efficient removal of oxidized AP sites. XPG could not substitute for FEN-1 in this pathway, supporting distinct roles for the structurally related FEN-1 and XPG enzymes.
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Klungland A, Lindahl T Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for DNase IV (FEN1). EMBO J. 16:1997;3341-3348. The long-patch BER pathway was reconstituted in vitro using Polβ or Polδ, FEN-1, PCNA and DNA ligase I. This FEN-1-dependent pathway was essential for the repair of reduced AP sites and is required for the efficient removal of oxidized AP sites. XPG could not substitute for FEN-1 in this pathway, supporting distinct roles for the structurally related FEN-1 and XPG enzymes.
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(1997)
EMBO J
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, pp. 3341-3348
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Klungland, A.1
Lindahl, T.2
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6
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0031574192
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Base excision repair enzyme family portrait: Integrating the structure and chemistry of an entire DNA repair pathway
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The introduction of a complete set of structures for a major BER pathway.
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Parikh SS, Mol CD, Tainer JA Base excision repair enzyme family portrait: integrating the structure and chemistry of an entire DNA repair pathway. Structure. 5:1997;1543-1550. The introduction of a complete set of structures for a major BER pathway.
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(1997)
Structure
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Parikh, S.S.1
Mol, C.D.2
Tainer, J.A.3
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0032100860
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Mammalian base excision repair and DNA polymerase β
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Wilson SH Mammalian base excision repair and DNA polymerase β Mutat Res. 407:1998;203-215.
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Mutat Res
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Wilson, S.H.1
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8
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0028934537
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Crystal structure and mutational analysis of human uracil-DNA glycosylase: Structural basis for specificity and catalysis
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Mol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I, Krokan HE, Tainer JA Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell. 80:1995;869-878.
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Cell
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Mol, C.D.1
Arvai, A.S.2
Slupphaug, G.3
Kavli, B.4
Alseth, I.5
Krokan, H.E.6
Tainer, J.A.7
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9
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0028959237
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The structural basis of specific base-excision repair by uracil-DNA glycosylase
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Savva R, McAuley-Hecht K, Brown T, Pearl L The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature. 373:1995;487-493.
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Nature
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Savva, R.1
McAuley-Hecht, K.2
Brown, T.3
Pearl, L.4
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10
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0342787062
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Base-excision repair initiation revealed by crystal structures and DNA-binding kinetics of human uracil-DNA glycosylase bound to DNA
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Crystal structures of wildtype and mutant UDG bound to U•G, U•A and AP site-containing DNA and DNA binding kinetics studies reveal a mechanism for active nucleotide flipping and support a model for DNA scanning by UDG. APE, which enhances UDG activity, is proposed to compete with UDG for its protected product AP site; thus AP sites are rarely exposed in the cell. AP site binding is hypothesized to couple the damage-specific and damage-general stages of BER without requiring direct protein-protein interactions.
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Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA Base-excision repair initiation revealed by crystal structures and DNA-binding kinetics of human uracil-DNA glycosylase bound to DNA. EMBO J. 17:1998;5412-5426. Crystal structures of wildtype and mutant UDG bound to U•G, U•A and AP site-containing DNA and DNA binding kinetics studies reveal a mechanism for active nucleotide flipping and support a model for DNA scanning by UDG. APE, which enhances UDG activity, is proposed to compete with UDG for its protected product AP site; thus AP sites are rarely exposed in the cell. AP site binding is hypothesized to couple the damage-specific and damage-general stages of BER without requiring direct protein-protein interactions.
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(1998)
EMBO J
, vol.17
, pp. 5412-5426
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Parikh, S.S.1
Mol, C.D.2
Slupphaug, G.3
Bharati, S.4
Krokan, H.E.5
Tainer, J.A.6
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11
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0029904839
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A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA
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Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature. 384:1996;87-92.
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Nature
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Slupphaug, G.1
Mol, C.D.2
Kavli, B.3
Arvai, A.S.4
Krokan, H.E.5
Tainer, J.A.6
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12
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0032213289
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Human mitochondrial uracil-DNA glycosylase preform (UNG1) is processed to two forms one of which is resistant to inhibition by AP-sites
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This paper reports the surprising result that UDG is differentially processed into two forms whose activities are both enhanced by APE, but differ in their inhibition by AP sites.
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Bharati S, Krokan HE, Kristiansen L, Otterlei M, Slupphaug G Human mitochondrial uracil-DNA glycosylase preform (UNG1) is processed to two forms one of which is resistant to inhibition by AP-sites. Nucleic Acids Res. 26:1998;4953-4959. This paper reports the surprising result that UDG is differentially processed into two forms whose activities are both enhanced by APE, but differ in their inhibition by AP sites.
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(1998)
Nucleic Acids Res
, vol.26
, pp. 4953-4959
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Bharati, S.1
Krokan, H.E.2
Kristiansen, L.3
Otterlei, M.4
Slupphaug, G.5
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13
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0030996226
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A sequence in the N-terminal region of human uracil-DNA glycosylase with homology to XPA interacts with the C-terminal part of the 34 kDa subunit of replication protein A
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Nagelhus T, Haug T, Singh KK, Keshav KF, Skorpen F, Otterlei M, Bharati S, Lindmo T, Benichou S, Benarous R, Krokan HE A sequence in the N-terminal region of human uracil-DNA glycosylase with homology to XPA interacts with the C-terminal part of the 34 kDa subunit of replication protein A. J Biol Chem. 272:1997;6561-6566.
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J Biol Chem
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Nagelhus, T.1
Haug, T.2
Singh, K.K.3
Keshav, K.F.4
Skorpen, F.5
Otterlei, M.6
Bharati, S.7
Lindmo, T.8
Benichou, S.9
Benarous, R.10
Krokan, H.E.11
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14
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0032538561
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Replication protein A stimulates long patch DNA base excision repair
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DeMott MS, Seymour Z, Bambara RA Replication protein A stimulates long patch DNA base excision repair. J Biol Chem. 273:1998;27492-27498.
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J Biol Chem
, vol.273
, pp. 27492-27498
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Demott, M.S.1
Seymour, Z.2
Bambara, R.A.3
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15
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0032168526
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PCNA binding proteins in Drosophila melanogaster: The analysis of a conserved PCNA binding domain
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Warbrick E, Heatherington W, Lane DP, Glover DM PCNA binding proteins in Drosophila melanogaster: the analysis of a conserved PCNA binding domain. Nucleic Acids Res. 26:1998;3925-3932.
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Nucleic Acids Res
, vol.26
, pp. 3925-3932
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Warbrick, E.1
Heatherington, W.2
Lane, D.P.3
Glover, D.M.4
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16
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0032493637
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Kinetics of the action of thymine DNA glycosylase
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Waters TR, Swann P Kinetics of the action of thymine DNA glycosylase. J Biol Chem. 273:1998;20007-20014.
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(1998)
J Biol Chem
, vol.273
, pp. 20007-20014
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Waters, T.R.1
Swann, P.2
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17
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0032498302
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Crystal structure of a G:T/U mismatch-specific DNA glycosylase: Mismatch recognition by complementary-strand interactions
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The crystal structures of MUG and a MUG-DNA complex reveal structural and functional homology between MUG and UDG, despite low sequence identity. The target nucleotide is flipped into the enzyme active site pocket of MUG, in a process resembling excision initiation by UDG. The co-crystal structure shows specific hydrogen bonds from the protein backbone to the mispaired guanine base that may account for MUG mismatch specificity.
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Barrett TE, Savva R, Panayotou G, Barlow T, Brown T, Pearl LH Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. Cell. 92:1998;117-129. The crystal structures of MUG and a MUG-DNA complex reveal structural and functional homology between MUG and UDG, despite low sequence identity. The target nucleotide is flipped into the enzyme active site pocket of MUG, in a process resembling excision initiation by UDG. The co-crystal structure shows specific hydrogen bonds from the protein backbone to the mispaired guanine base that may account for MUG mismatch specificity.
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(1998)
Cell
, vol.92
, pp. 117-129
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Barrett, T.E.1
Savva, R.2
Panayotou, G.3
Barlow, T.4
Brown, T.5
Pearl, L.H.6
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18
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0032516887
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Retinoic acid receptors interact physically and functionally with T:G mismatch-specific thymine-DNA glycosylase
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Um S, Harbers M, Benecke A, Pierrat B, Losson R, Chambon P Retinoic acid receptors interact physically and functionally with T:G mismatch-specific thymine-DNA glycosylase. J Biol Chem. 273:1998;20728-20736.
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J Biol Chem
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, pp. 20728-20736
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Um, S.1
Harbers, M.2
Benecke, A.3
Pierrat, B.4
Losson, R.5
Chambon, P.6
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19
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0030220956
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Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA-repair protein superfamily
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Nash HM, Bruner SD, Scharer OD, Kawate T, Addona TA, Spooner E, Lane WS, Verdine GL Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA-repair protein superfamily. Curr Biol. 6:1996;968-980.
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Curr Biol
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Nash, H.M.1
Bruner, S.D.2
Scharer, O.D.3
Kawate, T.4
Addona, T.A.5
Spooner, E.6
Lane, W.S.7
Verdine, G.L.8
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20
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0029119097
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Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure
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Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J. 14:1995;4108-4120.
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EMBO J
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Thayer, M.M.1
Ahern, H.2
Xing, D.3
Cunningham, R.P.4
Tainer, J.A.5
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21
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0031763884
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MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily
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MutY catalytic core, active site mutant and adenine complex crystal structures help to identify the active site specificity and catalytic residues of the enzyme and establish a specific DNA-binding orientation with implications for the entire HhH DNA glycosylase superfamily. These results provide the first direct observation of a base bound to a HhH DNA glycosylase active site and confirms that this superfamily of enzymes flip their target bases out of the DNA helix.
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Guan Y, Manuel RC, Arvai AS, Parikh SS, Mol CD, Miller JH, Lloyd RS, Tainer JA MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Nat Struct Biol. 5:1998;1058-1064. MutY catalytic core, active site mutant and adenine complex crystal structures help to identify the active site specificity and catalytic residues of the enzyme and establish a specific DNA-binding orientation with implications for the entire HhH DNA glycosylase superfamily. These results provide the first direct observation of a base bound to a HhH DNA glycosylase active site and confirms that this superfamily of enzymes flip their target bases out of the DNA helix.
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(1998)
Nat Struct Biol
, vol.5
, pp. 1058-1064
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Guan, Y.1
Manuel, R.C.2
Arvai, A.S.3
Parikh, S.S.4
Mol, C.D.5
Miller, J.H.6
Lloyd, R.S.7
Tainer, J.A.8
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22
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16044372779
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Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli
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Yamagata Y, Kato M, Odawara K, Tokuno Y, Nakashima Y, Matsushima N, Yasumura K, Tomita K, Ihara K, Fujii Yet al. Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli. Cell. 86:1996;311-319.
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Cell
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Yamagata, Y.1
Kato, M.2
Odawara, K.3
Tokuno, Y.4
Nakashima, Y.5
Matsushima, N.6
Yasumura, K.7
Tomita, K.8
Ihara, K.9
Fujii, Y.10
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23
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0030602838
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Structural basis for the excision repair of alkylation-damaged DNA
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Labahn J, Scharer OD, Long A, Ezaz-Nikpay K, Verdine GL, Ellenberger TE Structural basis for the excision repair of alkylation-damaged DNA. Cell. 86:1996;321-329.
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Cell
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, pp. 321-329
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Labahn, J.1
Scharer, O.D.2
Long, A.3
Ezaz-Nikpay, K.4
Verdine, G.L.5
Ellenberger, T.E.6
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24
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0030680251
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Life without DNA repair
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An informative review on DNA BER that describes various DNA repair knock-out experiments and discusses their role in defining the importance and mechanisms of DNA repair.
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Wilson DM III, Thompson LH Life without DNA repair. Proc Natl Acad Sci USA. 94:1997;12754-12757. An informative review on DNA BER that describes various DNA repair knock-out experiments and discusses their role in defining the importance and mechanisms of DNA repair.
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(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 12754-12757
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Wilson D.M. III1
Thompson, L.H.2
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25
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0032574770
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Activation of apurinic/apyrimidinic endonuclease in human cells by reactive oxygen species and its correlation with their adaptive response to genotoxicity of free radicals
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The authors report the exciting discovery that APE is selectively upregulated by reactive oxygen species, but not by UV light or alkylating agents. The implications of this, which include the critical role of APE in creating an adaptive response to exogenous mutagens, contribute to our understanding of the various cellular processes in which APE participates.
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Ramana CV, Boldogh I, Izumi T, Mitra S Activation of apurinic/apyrimidinic endonuclease in human cells by reactive oxygen species and its correlation with their adaptive response to genotoxicity of free radicals. Proc Natl Acad Sci USA. 95:1998;5061-5066. The authors report the exciting discovery that APE is selectively upregulated by reactive oxygen species, but not by UV light or alkylating agents. The implications of this, which include the critical role of APE in creating an adaptive response to exogenous mutagens, contribute to our understanding of the various cellular processes in which APE participates.
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(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 5061-5066
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Ramana, C.V.1
Boldogh, I.2
Izumi, T.3
Mitra, S.4
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26
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0030728449
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The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites
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The crystal structure of human AP endonuclease (alternatively called HAP1 and REF1) at 2.2 Å resolution shows a significant similarity to ExoIII and DNase I. Importantly, structural analysis suggests a mechanism for AP site binding and cleavage catalysis, with implications for pathway interactions.
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Gorman MA, Morera S, Rothwell DG, deLa Fortelle E, Mol CD, Tainer JA, Hickson ID, Freemont PS The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. EMBO J. 16:1997;6548-6558. The crystal structure of human AP endonuclease (alternatively called HAP1 and REF1) at 2.2 Å resolution shows a significant similarity to ExoIII and DNase I. Importantly, structural analysis suggests a mechanism for AP site binding and cleavage catalysis, with implications for pathway interactions.
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(1997)
EMBO J
, vol.16
, pp. 6548-6558
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Gorman, M.A.1
Morera, S.2
Rothwell, D.G.3
Dela Fortelle, E.4
Mol, C.D.5
Tainer, J.A.6
Hickson, I.D.7
Freemont, P.S.8
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27
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0028923440
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Structure and function of the multifunctional DNA-repair enzyme exonuclease III
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Mol CD, Kuo CF, Thayer MM, Cunningham RP, Tainer JA Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature. 374:1995;381-386.
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Nature
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, pp. 381-386
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Mol, C.D.1
Kuo, C.F.2
Thayer, M.M.3
Cunningham, R.P.4
Tainer, J.A.5
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28
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0001882582
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Structural phylogenetics of DNA base excision repair
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F. Eckstein, & D.M.J. Lilley. Berlin: Springer. An overview of repair enzyme structures. The authors introduce the concept of structural phylogenetics as a new approach for identifying surface conservation outside active sites that probably contribute to the short-lived protein-protein interactions regulating DNA repair pathways.
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Mol CD, Parikh SS, Lo TP, Tainer JA Structural phylogenetics of DNA base excision repair. Eckstein F, Lilley DMJ Nucleic Acids & Molecular Biology, vol 12. 1998;29-69 Springer, Berlin. An overview of repair enzyme structures. The authors introduce the concept of structural phylogenetics as a new approach for identifying surface conservation outside active sites that probably contribute to the short-lived protein-protein interactions regulating DNA repair pathways.
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(1998)
Nucleic Acids & Molecular Biology, Vol 12
, pp. 29-69
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Mol, C.D.1
Parikh, S.S.2
Lo, T.P.3
Tainer, J.A.4
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29
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0038342180
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Specific binding of a designed abasic site analog to multiple DNA glycosylases
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Abasic site analogs are shown to bind specifically to multiple DNA glycosylases. A designed pyrrolidine abasic site analog binds especially tightly and will probably be valuable in the study of stable glycosylase-DNA complexes.
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Scharer OD, Nash HM, Jiricny J, Laval J, Verdine GL Specific binding of a designed abasic site analog to multiple DNA glycosylases. J Biol Chem. 273:1998;8592-8597. Abasic site analogs are shown to bind specifically to multiple DNA glycosylases. A designed pyrrolidine abasic site analog binds especially tightly and will probably be valuable in the study of stable glycosylase-DNA complexes.
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J Biol Chem
, vol.273
, pp. 8592-8597
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Scharer, O.D.1
Nash, H.M.2
Jiricny, J.3
Laval, J.4
Verdine, G.L.5
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30
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0030030379
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Requirement of mammalian DNA polymerase β in base-excision repair
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Sobol RW, Horton JK, Kühn R, Gu H, Singhal RK, Prasad R, Rajewsky K, Wilson SH Requirement of mammalian DNA polymerase β in base-excision repair. Nature. 379:1996;183-186.
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Nature
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Sobol, R.W.1
Horton, J.K.2
Kühn, R.3
Gu, H.4
Singhal, R.K.5
Prasad, R.6
Rajewsky, K.7
Wilson, S.H.8
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Excision of deoxyribose phosphate residues by DNA polymerase β during repair
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Matsumoto Y, Kim K Excision of deoxyribose phosphate residues by DNA polymerase β during repair. Science. 269:1995;699-702.
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Science
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Matsumoto, Y.1
Kim, K.2
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0030930760
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Crystal structure of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
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Crystal structures of human Polβ reveal the intermediates of the one-nucleotide gap-filling reaction used in BER. These include a binary complex with gapped DNA, a ternary complex including ddCTP and a binary product complex containing only nicked DNA. The structures show that human Polβ kinks DNA by 90° and creates the active site by closing around the substrate. The 90° kink is hypothesized to be important in the checking mechanism.
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Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H Crystal structure of human DNA polymerase β complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry. 36:1997;11205-11215. Crystal structures of human Polβ reveal the intermediates of the one-nucleotide gap-filling reaction used in BER. These include a binary complex with gapped DNA, a ternary complex including ddCTP and a binary product complex containing only nicked DNA. The structures show that human Polβ kinks DNA by 90° and creates the active site by closing around the substrate. The 90° kink is hypothesized to be important in the checking mechanism.
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Biochemistry
, vol.36
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Sawaya, M.R.1
Prasad, R.2
Wilson, S.H.3
Kraut, J.4
Pelletier, H.5
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33
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0032005866
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Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes
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An insightful review into the commonalities and differences amongst the four polymerase families for which a crystal structure has been determined: Polα-like, Pol I-like, terminal transferases and reverse transcriptases.
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Brautigam CA, Steitz TA Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr Opin Struct Biol. 8:1998;54-63. An insightful review into the commonalities and differences amongst the four polymerase families for which a crystal structure has been determined: Polα-like, Pol I-like, terminal transferases and reverse transcriptases.
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Curr Opin Struct Biol
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, pp. 54-63
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Brautigam, C.A.1
Steitz, T.A.2
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34
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DNA polymerase β: Multiple conformational changes in the mechanism of catalysis
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Zhong X, Patel SS, Werneburg BG, Tsai MD DNA polymerase β: multiple conformational changes in the mechanism of catalysis. Biochemistry. 36:1997;11891-11900.
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(1997)
Biochemistry
, vol.36
, pp. 11891-11900
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Zhong, X.1
Patel, S.S.2
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An informative short review on the recently determined Polβ, T7 DNA polymerase and Bacillus stearothermophilus DNA polymerase crystal structures that lucidly comments on the conformational dynamics, active sites, binding, processivity and fidelity of these enzymes.
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Kunkel TA, Wilson SH DNA polymerases on the move. Nat Struct Biol. 5:1998;95-99. An informative short review on the recently determined Polβ, T7 DNA polymerase and Bacillus stearothermophilus DNA polymerase crystal structures that lucidly comments on the conformational dynamics, active sites, binding, processivity and fidelity of these enzymes.
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Specific interaction of DNA polymerase Qb and DNA ligase I in a multiprotein base excision repair complex from bovine testis
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Functional domains of an ATP-dependent DNA ligase
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in press. The independent expression of the two T7 DNA ligase domains allowed the characterization of their individual properties and an assessment of their interaction. Together, the data suggest that the two domains interact in order to catalyze adenylation and undergo a conformational change in order to create the catalytically competent complex
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Doherty AJ, Wigley DB. Functional domains of an ATP-dependent DNA ligase. J Mol Biol 1999, in press. The independent expression of the two T7 DNA ligase domains allowed the characterization of their individual properties and an assessment of their interaction. Together, the data suggest that the two domains interact in order to catalyze adenylation and undergo a conformational change in order to create the catalytically competent complex.
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Interaction of human apurinic endonuclease and DNA polymerase β in the base excision repair pathway
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Yeast two-hybrid analysis identified direct protein-protein interactions between APE and Polβ. APE also enhances the Polβ dRPase activity. Interestingly, no direct protein-protein interactions were detected between APE and human alkyl-purine DNA glycosylase.
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Bennett RAO, Wilson DM III, Wong D, Demple B Interaction of human apurinic endonuclease and DNA polymerase β in the base excision repair pathway. Proc Natl Acad Sci USA. 94:1997;7166-7169. Yeast two-hybrid analysis identified direct protein-protein interactions between APE and Polβ. APE also enhances the Polβ dRPase activity. Interestingly, no direct protein-protein interactions were detected between APE and human alkyl-purine DNA glycosylase.
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Wilson D.M. III2
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41
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0028862933
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Characterization of the XRCC1-DNA ligase III complex in vitro and its absence from mutant hamster cells
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Caldecott KW, Tucker JD, Stanker LH, Thompson LH Characterization of the XRCC1-DNA ligase III complex in vitro and its absence from mutant hamster cells. Nucleic Acids Res. 23:1995;4836-4843.
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Reconstitution of DNA base excision-repair with purified human proteins: Interaction between DNA polymerase β and the XRCC1 protein
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Kubota Y, Nash RA, Klungland A, Schär P, Barnes DE, Lindahl T Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase β and the XRCC1 protein. EMBO J. 15:1996;6662-6670.
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43
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XRCC1 is specifically associated with poly(ADP-ribose) polymerase and negatively regulates its activity following DNA damage
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Using PARP as bait in a yeast two-hybrid screen of a HeLa cDNA library allowed the detection of an interaction between PARP and XRCC1. This PARP-XRCC1 interaction was confirmed in human cells and was hypothesized to be responsible for targeting damage-general BER enzymes to the site of DNA strand breaks.
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Masson M, Niedergang C, Schreiber V, Muller S, deMurcia JMD, deMurcia G XRCC1 is specifically associated with poly(ADP-ribose) polymerase and negatively regulates its activity following DNA damage. Mol Cell Biol. 18:1998;3563-3571. Using PARP as bait in a yeast two-hybrid screen of a HeLa cDNA library allowed the detection of an interaction between PARP and XRCC1. This PARP-XRCC1 interaction was confirmed in human cells and was hypothesized to be responsible for targeting damage-general BER enzymes to the site of DNA strand breaks.
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Masson, M.1
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44
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Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human FEN-1
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Hosfield DJ, Frank G, Weng Y, Tainer JA, Shen B Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human FEN-1. J Biol Chem. 273:1998;27154-27161.
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The crystal structure of P. furiosus FEN-1 provides a model for DNA flap junction binding by FEN-1 and identifies a H3TH DNA-binding motif. A model for FEN-1 binding to PCNA during lagging-strand DNA synthesis suggests a hypothesis regarding the cause of the DNA repeat expansions that are seen in some cancers and heritable genetic diseases.
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Hosfield DJ, Mol CD, Shen B, Tainer JA Crystal structure of the DNA repair and replication endonuclease and exonuclease FEN-1: implications for coupling DNA and PCNA binding to enzymatic activity. Cell. 95:1998;135-146. The crystal structure of P. furiosus FEN-1 provides a model for DNA flap junction binding by FEN-1 and identifies a H3TH DNA-binding motif. A model for FEN-1 binding to PCNA during lagging-strand DNA synthesis suggests a hypothesis regarding the cause of the DNA repeat expansions that are seen in some cancers and heritable genetic diseases.
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The crystal structure of flap endonuclease-1 from Methanococcus jannaschii
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The crystal structure of M. jannaschii FEN-1 suggests that single-stranded DNA threads through a flexible enzyme loop. Deletion mutants of this loop show significantly decreased nuclease activity and specificity. A model of DNA flap junction binding is presented.
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Hwang KY, Baek K, Kim HY, Cho Y The crystal structure of flap endonuclease-1 from Methanococcus jannaschii. Nat Struct Biol. 5:1998;707-713. The crystal structure of M. jannaschii FEN-1 suggests that single-stranded DNA threads through a flexible enzyme loop. Deletion mutants of this loop show significantly decreased nuclease activity and specificity. A model of DNA flap junction binding is presented.
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Shen B, Qui J, Hosfield DJ, Tainer JA Flap endonuclease homologues identified in archaebacteria exist as independent proteins. Trends Biochem Sci. 23:1998;171-173.
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Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA
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51
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BRCA1 required for transcription-coupled repair of oxidative DNA damage
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This surprising and exciting result shows that mouse embryonic stem cells deficient in BRCA1 are defective in transcription-coupled repair of oxidative DNA damage. This suggests that BRCA1 participates in transcription-coupled repair of oxidative DNA damage, at least some of which proceeds through BER.
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Gowen LC, Avrutskaya AV, Latour AM, Koller BH, Leadon SA BRCA1 required for transcription-coupled repair of oxidative DNA damage. Science. 281:1998;1009-1012. This surprising and exciting result shows that mouse embryonic stem cells deficient in BRCA1 are defective in transcription-coupled repair of oxidative DNA damage. This suggests that BRCA1 participates in transcription-coupled repair of oxidative DNA damage, at least some of which proceeds through BER.
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Science
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Gowen, L.C.1
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Latour, A.M.3
Koller, B.H.4
Leadon, S.A.5
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52
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0032555571
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Purification and characterization of human NTH1, a homolog of Escherichia coli endonuclease III. Direct identification of Lys-212 as the active nucleophilic residue
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Ikeda S, Biswas T, Roy R, Izumi T, Boldogh I, Kurosky A, Sarker AH, Seki S, Mitra S Purification and characterization of human NTH1, a homolog of Escherichia coli endonuclease III. Direct identification of Lys-212 as the active nucleophilic residue. J Biol Chem. 273:1998;21585-21593.
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Ikeda, S.1
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Kurosky, A.6
Sarker, A.H.7
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Cunningham RP DNA repair: caretakers of the genome? Curr Biol. 7:1997;576-579.
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MutY DNA glycosylase: Base release and intermediate complex formation
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Zharkov DO, Grollman AP MutY DNA glycosylase: base release and intermediate complex formation. Biochemistry. 37:1998;12384-12394.
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Base flipping
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A comprehensive and informative review of the known enzymes that are proposed to flip bases out of the DNA double helix.
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Cheng X, Roberts RJ Base flipping. Annu Rev Biochem. 67:1998;181-198. A comprehensive and informative review of the known enzymes that are proposed to flip bases out of the DNA double helix.
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Crystal structure of a human alklybase-DNA repair enzyme complexed to DNA: Mechanisms for nucleotide flipping and base excision
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This co-crystal structure reveals a new DNA glycosylase fold that shares several of the themes discussed in this review. A tyrosine intercalates into the DNA through the minor groove, causing the abasic pyrrolidine nucleotide to flip into the enzyme active site. Hypotheses for DNA scanning and enzyme chemistry are presented.
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Lau AY, Scharer OD, Samson L, Verdine GL, Ellenberger T Crystal structure of a human alklybase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision. Cell. 95:1998;249-258. This co-crystal structure reveals a new DNA glycosylase fold that shares several of the themes discussed in this review. A tyrosine intercalates into the DNA through the minor groove, causing the abasic pyrrolidine nucleotide to flip into the enzyme active site. Hypotheses for DNA scanning and enzyme chemistry are presented.
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Cell
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Lau, A.Y.1
Scharer, O.D.2
Samson, L.3
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57
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0032476599
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Structure of an XRCC1 BRCT domain: A new protein-protein interaction module
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The authors present the first structure of a BRCT (BRCA1 C terminus) domain. The structure reveals a compact, autonomously folded α/β domain. The BRCT homodimer structure suggests potential protein-protein interaction sites that are likely to be key to the formation of the biologically relevant heterodimers and provides a model for BRCT domains from other enzymes involved in DNA repair, replication and the cell cycle.
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Zhang X, Morera S, Bates PA, Whitehead PC, Coffer AI, Hainbucher K, Nash RA, Sternberg MJ, Lindahl T, Freemont PS Structure of an XRCC1 BRCT domain: a new protein-protein interaction module. EMBO J. 17:1998;6404-6411. The authors present the first structure of a BRCT (BRCA1 C terminus) domain. The structure reveals a compact, autonomously folded α/β domain. The BRCT homodimer structure suggests potential protein-protein interaction sites that are likely to be key to the formation of the biologically relevant heterodimers and provides a model for BRCT domains from other enzymes involved in DNA repair, replication and the cell cycle.
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EMBO J
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Zhang, X.1
Morera, S.2
Bates, P.A.3
Whitehead, P.C.4
Coffer, A.I.5
Hainbucher, K.6
Nash, R.A.7
Sternberg, M.J.8
Lindahl, T.9
Freemont, P.S.10
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