Envisioning the fourth dimension of the genetic code: The structural biology of macromolecular recognition and conformational switching in DNA repair

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 65, Issue , 2000, Pages 113-126

  Hopfner, K P ^a   Parikh, S S ^a   Tainer, J A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFERENCE PAPER; DNA CONFORMATION; DNA DAMAGE; DNA POLYMORPHISM; DNA REPAIR; DNA STRUCTURE; EXCISION REPAIR; MACROMOLECULE; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA BINDING; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETIC CODE; GENETICS; HUMAN; REVIEW; AMINO ACID SEQUENCE; ARTICLE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; DOUBLE STRANDED DNA BREAK; NONHUMAN; PROTEIN FUNCTION; PROTEIN PROCESSING; PROTEIN STRUCTURE;

DNA; DNA BASE; DNA GLYCOSYLTRANSFERASE; DNA LIGASE; MRE11 PROTEIN; NIBRIN; RAD50 PROTEIN;

ANIMAL; DNA; DNA REPAIR; GENETIC CODE; HUMAN; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; SUPPORT, NON-U.S. GOV'T; SUPPORT, U.S. GOV'T, P.H.S.;

EID: 0034437341     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2000.65.113     Document Type: Conference Paper

References (101)

1. Identification of new genes required for meiotic recombination in Saccharomyces cerevisiae
2. Analysis of wild-type and rad50 mutants of yeast suggests an intimate relationship between meiotic chromosome synapsis and recombination
3. Conserved domains in DNA repair proteins and evolution of repair systems
4. Powering the ABC transporters: The 2.5 Å crystal structure of the ABC domain of RBSA
5. Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway
6. Deletions at stalled replication forks occur by two different pathways
7. Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing
8. The Mre11-Rad50-Xrs2 protein complex facilitates homologous recombination-based double-strand break repair in Saccharomyces cerevisiae
9. Characterization of the XRCC1-DNA ligase III complex in vitro and its absence from mutant hamster cells
10. The hMre11/hRad50 protein complex and Nijmegen breakage syndrome: Linkage of double-strand break repair to the cellular DNA damage response
11. The Saccharomyces cerevisiae mre11(ts) allele confers a separation of DNA repair and telomere maintenance functions
12. Review: SMCs in the world of chromosome biology - From prokaryotes to higher eukaryotes
13. The SbcCD nuclease of Escherichia coli is a structural maintenance of chromosomes (SMC) family protein that cleaves hairpin DNA
14. Overexpression, purification, and characterization of the SbcCD protein from Escherichia coli
15. Defective transcription-coupled repair of oxidative base damage in Cockayne syndrome patients from XP group G
16. DNA end-joining: From yeast to man
17. DNA glycosylases
18. Overproduction, solubilization, and reconstitution of the maltose transport system from Escherichia coli
19. Mutation of a single MalK subunit severely impairs maltose transport activity in Escherichia coli
20. Exonuclease III and endonuclease IV remove 3′ blocks from DNA synthesis primers in H2O2-damaged Escherichia coli
21. ATP-dependent transport systems in bacteria and humans: Relevance to cystic fibrosis and multidrug resistance
22. Human Rad50 is physically associated with hMre11: Identification of a conserved multiprotein complex implicated in recombinational DNA repair
23. Out of the shadows and into the light: The emergence of DNA repair
24. Distinct roles of two separable in vitro activities of yeast mre11 in mitotic and meiotic recombination
25. Control of CFTR channel gating by phosphorylation and nucleotide hydrolysis
26. DNA double strand breaks and the RAD50-RAD57 genes in Saccharomyces
27. Recent advances in understanding V(D)J recombination
28. Sequence-specific DNA binding by Ku autoantigen and its effects on transcription
29. Mre11 and Ku70 interact in somatic cells, but are differentially expressed in early meiosis
30. The many interfaces of Mre11
31. Recombination: A frank view of exchanges and vice versa
32. ABC-ATPases, adaptable energy generators fueling transmembrane movement of a variety of molecules in organisms from bacteria to humans
33. DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA
34. Closing the ring: Links between SMC proteins and chromosome partitioning, condensation, and supercoiling
35. Mre11 and Rad50 from Pyrococcus furiosus: Cloning and biochemical characterization reveal an evolutionary conserved multiprotein machine
36. Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double strand break and the ABC-ATPase superfamily
37. Crystal structure of the ATP-binding subunit of an ABC transporter
38. Subunit interactions in ABC transporters: Towards a functional architecture
39. Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae
40. Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase
41. 13S Condensin actively reconfigures DNA by introducing global positive writhe: Implications for chromosome condensation
42. Abasic sites stimulate double-stranded DNA cleavage mediated by topoisomerase II. DNA lesions as endogenous topoisomerase II poisons
43. DNA glycosylases in the base excision repair of DNA
44. Reconstitution of DNA base excision-repair with purified human proteins: Interaction between DNA polymerase beta and the XRCC1 protein
45. Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: Mechanisms for nucleotide flipping and base excision
46. Transcription-coupled repair of DNA damage: Unanticipated players, unexpected complexities
47. Apurinic sites as mutagenic intermediates
48. Instability and decay of the primary structure of DNA
49. Quality control by DNA repair
50. Characterisation of transport through the periplasmatic histidine permease using proteoliposomes reconstituted by dialysis
51. Modulation of ATPase activity by physical disengagement of the ATP-binding domains of an ABC transporter, the histidine permease
52. The initiation of DNA base excision repair of dipyrimidine photoproducts
53. Covalent modification of human P-glycoprotein mutants containing a single cysteine in either nucleotide-binding fold abolishes drug-stimulated ATPase activity
54. Disruption of mRad50 causes embryonic stem cell lethality, abnormal embryonic development, and sensitivity to ionizing radiation
55. Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair
56. The symmetrical structure of structural maintenance of chromosomes (SMC) and MukB proteins: Long, antiparallel coiled coils, folded at a flexible hinge
57. DNA double-strand breaks caused by replication arrest
58. DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination
59. Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: Protein mimicry of DNA
60. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae
61. mre11S - A yeast mutation that blocks double-strand-break processing and permits nonhomologous synapsis in meiosis
62. In situ visualization of DNA double strand break repair in human fibroblasts
63. One intact ATP-binding subunit is sufficient to support ATP hydrolysis and translocation in an ABC transporter, the histidine permease
64. Base excision repair enzyme family portrait: Integrating the structure and chemistry of an entire DNA repair pathway
65. Envisioning the molecular choreography of DNA base excision repair
66. Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA
67. Uracil-DNA glycosylase-DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects
68. The 3′ to 5′ exonuclease activity of Mre 11 facilitates repair of DNA double-strand breaks
69. Nbs1 potentiates ATP-driven DNA unwinding and endonuclease cleavage by the Mre11/Rad50 complex
70. A mechanistic basis for Mre11-directed DNA joining at microhomologies
71. The RAD52 epistasis group in mammalian double strand break repair
72. Illegitimate recombination induced by DNA double-strand breaks in a mammalian chromosome
73. Imbalanced base excision repair increases spontaneous mutation and alkylation sensitivity in Escherichia coli
74. Trapping of mammalian topoisomerase I and recombinations induced by damaged DNA containing nicks or gaps. Importance of DNA end phosphorylation and camptothecin effects
75. Effects of uracil incorporation, DNA mismatches, and abasic sites on cleavage and religation activities of mammalian topoisomerase I
76. Induction of reversible complexes between eukaryotic DNA topoisomerase I and DNA-containing oxidative base damages. 7,8-dihydro-8-oxoguanine and 5-hydroxycytosine
77. Specific interaction of DNA polymerase beta and DNA ligase I in a multiprotein base excision repair complex from bovine testis
78. Mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase
79. RAD50 protein of S. cerevisiae exhibits ATP-dependent DNA binding
80. Holding damaged DNA together
81. Illegitimate recombination in mammalian cells
82. The SMC proteins and the coming of age of the chromosome scaffold hypothesis
83. Homologous recombination and the roles of double-strand breaks
84. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA
85. The DNA double-strand break repair gene hMRE11 is mutated in individuals with an ataxia-telangiectasia-like disorder
86. Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase
87. Structural maintenance of chromosomes (SMC) proteins: Conserved molecular properties for multiple biological functions
88. Biological implication from structures of DNA repair proteins
89. XRCC1 keeps DNA from getting stranded
90. Nuclease activities in a complex of human recombination and DNA repair factors Rad50, Mre11, and p95
91. Complex formation and functional versatility of Mre11 of budding yeast in recombination
92. Crystal structure of the N-terminal domain of MukB: A protein involved in chromosome partitioning
93. Binding of double-strand breaks in DNA by human Rad52 protein
94. Nibrin, a novel DNA double-strand break repair protein, is mutated in Nijmegen breakage syndrome
95. DNA damage produced by ionizing radiation in mammalian cells: Identities, mechanisms of formation, and repairability
96. Human thymine DNA glycosylase binds to apurinic sites in DNA but is displaced by human apurinic endonuclease 1
97. Life without DNA repair
98. Mammalian base excision repair and DNA polymerase β
99. Mre11 is essential for the maintenance of chromosomal DNA in vertebrate cells
100. Association of BRCA1 with the hRad50-hMre11-p95 complex and the DNA damage response