Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypass

DNA Repair

Volumn 1, Issue 5, 2002, Pages 343-358

  Boudsocq, François ^a   Ling, Hong ^b   Yang, Wei ^b   Woodgate, Roger ^a  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

DNA replication; Pol ; Pol ; Pol ; Pol IV; Pol V; Rev1

Indexed keywords

AMINO ACID; DEOXYRIBONUCLEOPROTEIN; DNA DIRECTED DNA POLYMERASE ETA; DNA POLYMERASE; ISOPROTEIN; PROTEIN DINB; PROTEIN UMUC; REV PROTEIN; RNA DIRECTED RNA POLYMERASE; UNCLASSIFIED DRUG; DNA DIRECTED DNA POLYMERASE;

AMINO ACID SUBSTITUTION; DNA DAMAGE; DNA REPLICATION; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME MODIFICATION; GENE MUTATION; GENETIC SELECTION; MISSENSE MUTATION; MOLECULAR MECHANICS; MUTAGENESIS; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN TERTIARY STRUCTURE; SHORT SURVEY; STRUCTURE ACTIVITY RELATION; AMINO ACID SEQUENCE; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; DNA REPAIR; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; HUMAN; MOLECULAR GENETICS; MULTIGENE FAMILY; PROTEIN CONFORMATION; PROTEIN FOLDING; REVIEW; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMAL; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; ESCHERICHIA COLI; HUMAN; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTATION, MISSENSE; PROTEIN CONFORMATION; PROTEIN FOLDING; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURE-ACTIVITY RELATIONSHIP; SUPPORT, NON-U.S. GOV'T; ANIMALS; HUMANS;

EID: 0037198267     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1568-7864(02)00019-8     Document Type: Short Survey

References (102)

1. Mutants of yeast defective in mutation induced by ultraviolet light
2. Isolation and characterization of mutants of Escherichia coli deficient in induction of mutations by ultraviolet light
3. Uvm mutants of Escherichia coli K12 deficient in UV mutagenesis. Part I. Isolation of uvm mutants and their phenotypical characterization in DNA repair and mutagenesis
4. The REV1 gene of Saccharomyces cerevisiae: Isolation, sequence and functional analysis
5. Structural analysis of the umu operon required for inducible mutagenesis in Escherichia coli
6. UmuDC and mucAB operons whose products are required for UV light and chemical-induced mutagenesis: UmuD, MucA and LexA products share homology
7. Sequence analysis of the Salmonella typhimurium LT2 umuDC operon
8. Structural characterization of the Salmonella typhimurium LT2 umu operon
9. DinP, a new gene in Escherichia coli, whose product shows similarities to UmuC and its homologues
10. Salmonella typhimurium has two homologous but different umuDC operons: Cloning of a new umuDC-like operon (samAB) present in a 60 MDa cryptic plasmid of S. typhimurium
11. A rapid method for cloning mutagenic DNA repair genes: Isolation of umu-complementing genes from multidrug resistance plasmids R391, R446b and R471a
12. Characterization of the umu-complementing operon from R391
13. Resistance to ultraviolet light in Pseudomonas syringae: Sequence and functional analysis of the plasmid-encoded rulAB genes
14. Identification of a DinB/UmuC homolog in the archeon Sulfolobus solfataricus
15. Novel human and mouse homologs of Saccharomyces cerevisiae DNA polymerase η
16. Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily
17. The Y-family of DNA polymerases
18. The two-step model of bacterial UV mutagenesis
19. Deoxycytidyl transferase activity of yeast Rev1 protein
20. The Saccharomyces cerevisiae RAD30 gene, a homologue of Escherichia coli dinB and umuC, is DNA damage inducible and functions in a novel error-free post-replication repair mechanism
21. Deletion of the Saccharomyces cerevisiae gene RAD30 encoding an Escherichia coli DinB homolog confers UV radiation sensitivity and altered mutability
22. Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase pol η
23. The dinB gene encodes an novel Escherichia coli DNA polymerase (DNA pol IV) involved in mutagenesis
24. 2′ C is an error-prone DNA polymerase, Escherichia coli DNA pol V
25. The mutagenesis protein UmuC is a DNA polymerase activated by UmuD′ RecA and SSB and is specialized for translesion replication
26. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η
27. HRAD30 mutations in the variant form of xeroderma pigmentosum
28. Pol ι, a remarkably error-prone human DNA polymerase
29. Eukaryotic polymerases ι and ζ act sequentially to bypass DNA lesions
30. Preferential incorporation of G opposite template T by the low-fidelity human DNA polymerase ι
31. The human DINB1 gene encodes the DNA polymerase pol θ
32. Error-pone bypass of certain DNA lesions by the human DNA polymerase κ
33. Error-free and error-prone lesion bypass by human DNA polymerase κ in vitro
34. Purification and characterization of pol κ, a DNA polymerase encoded by the human DINB1 gene
35. Compilation and alignment of DNA polymerase sequences
36. Compilation, alignment and phylogenetic relationships of DNA polymerases
37. Archaeal DNA replication: Identifying the pieces to solve a puzzle
38. Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain
39. Structure of the catalytic core of S. cerevisiae DNA polymerase η implications for translesion DNA synthesis
40. Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication
41. Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus
42. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
43. Structure of the replicating complex of a pol α family DNA polymerase
44. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance
45. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
46. 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
47. DNA polymerases: Structural diversity and common mechanisms
48. Low fidelity DNA synthesis by human DNA polymerase η
49. Proofreading of DNA polymerase η-dependent replication errors
50. Fidelity of human DNA polymerase η
51. Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): An archaeal DNA polymerase with lesion-bypass properties akin to eukaryotic pol η
52. Synthetic activity of Sso DNA polymerase Y1, an archaeal DinB-like DNA polymerase, is stimulated by processivity factors proliferating cell nuclear antigen and replication factor C
53. Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis
54. Escherichia coli DNA polymerase IV mutator activity: Genetic requirements and mutational specificity
55. All three SOS-inducible DNA polymerases (pols II, IV and V) are involved in induced mutagenesis
56. Fidelity and processivity of DNA synthesis by DNA polymerase κ, the product of the human DINB1 gene
57. Human DNA polymerase ι promiscuous mismatch extension
58. UmuC mutagenesis protein of Escherichia coli: Purification and interaction with UmuD and UmuD′
59. Purification of a soluble UmuD′C complex from Escherichia coli: Cooperative binding of UmuD′C to single-stranded DNA
60. A model for SOS-lesion targeted mutations in E. coli involving pol V, RecA, SSB and β sliding clamp
61. Lesion bypass by the Escherichia coli DNA polymerase V requires assembly of a RecA nucleoprotein filament
62. The processivity factor β controls DNA polymerase IV traffic during spontaneous mutagenesis and translesion synthesis in vivo
63. Physical and functional interactions of human DNA polymerase η with PCNA
64. Interaction with PCNA is essential for yeast DNA polymerase η function
65. Targeting of human DNA polymerase ι to the replication machinery via interaction with PCNA
66. Stimulation of DNA synthesis activity of human DNA polymerase κ by PCNA
67. Escherichia coli umuDC mutants: DNA sequence alterations and UmuD cleavage
68. Isolation and characterization of novel plasmid-encoded umuC mutants
69. Mutagenic DNA repair in Escherichia coli. Part XX. Overproduction of UmuD′ protein results in suppression of the umuC36 mutation in excision defective bacteria
70. In vivo stability of the Umu mutagenesis proteins: A major role for RecA
71. Regulation of SOS mutagenesis by proteolysis
72. The appearance of the UmuD′C protein complex in Escherichia coli switches repair from homologous recombination to SOS mutagenesis
73. - recombination by the mutagenesis complex UmuD′C
74. Specific RecA amino acid changes affect RecA-UmuD′C interaction
75. Modulation of recombination function by the mutagenic UmuD′C protein complex
76. 2′C complex (DNA pol V) on RecA-ssDNA filaments
77. Specific amino acid changes enhance the anti-recombination activity of the UmuD′C complex
78. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems
79. SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification
80. 2′ C mutagenic complex and RecA
81. The β-clamp targets DNA polymerase IV to DNA and strongly increases its processivity
82. The ring-type polymerase sliding clamp family
83. Three-dimensional structure of the β subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp
84. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA
85. Crystal structure of the processivity clamp loader γ complex of E. coli DNA polymerase III
86. Clamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC
87. Domain structure, localization and function of DNA polymerase η, defective in xeroderma pigmentosum variant cells
88. The complete genome of the crenarchaeon Sulfolobus solfataricus P2
89. Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7
90. Three proliferating cell nuclear antigen-like proteins found in the hyperthermophilic archaeon Aeropyrum pernix: Interactions with the two DNA polymerases
91. Mechanisms of dCMP transferase reactions catalyzed by mouse Rev1 protein
92. Evidence for a second function for Saccharomyces cerevisiae Rev1 protein
93. Acidic residues critical for the activity and biological function of yeast DNA polymerase η
94. Genomic structure, chromosomal localization and identification of mutations in the xeroderma pigmentosum variant (XPV) gene
95. Molecular analysis of mutations in DNA polymerase η in xeroderma pigmentosum variant patients
96. Mutations in human DNA polymerase η motif II alter bypass of DNA lesions
97. Unique misinsertion specificity of pol ι may decrease the mutagenic potential of deaminated cytosines
98. 2C complex involved in a DNA damage checkpoint control
99. Ribbon model of macromolecules
100. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons