Structural basis for proofreading during replication of the Escherichia coli chromosome

Structure

Volumn 10, Issue 4, 2002, Pages 535-546

  Hamdan, Samir ^a   Carr, Paul D ^a   Brown, Susan E ^a   Ollis, David L ^a   Dixon, Nicholas E ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Binuclear metallohydrolase; DNA polymerase III; DNA replication; DnaQ; Exonuclease (3 5 ); Manganese metalloenzyme; X ray crystallography

Indexed keywords

DNA DIRECTED DNA POLYMERASE GAMMA; EXONUCLEASE; MANGANESE; THYMIDINE PHOSPHATE; WATER;

ARTICLE; BACTERIAL CHROMOSOME; CHROMOSOME REPLICATION; DNA PROTEIN COMPLEX; DNA REPLICATION; ESCHERICHIA COLI; PH; PRIORITY JOURNAL; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; CHROMOSOMES, BACTERIAL; CRYSTALLOGRAPHY, X-RAY; DNA POLYMERASE III; DNA REPLICATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EXODEOXYRIBONUCLEASE V; EXODEOXYRIBONUCLEASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0036229246     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(02)00738-4     Document Type: Article

References (80)

1. Fidelity mechanisms in DNA replication
2. DNA replication fidelity
3. Spontaneous mutation
4. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
5. Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP
6. Crystal structure of Thermus aquaticus DNA polymerase
7. 2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions
8. Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 Å resolution
9. Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69
10. Crystal structure of an archaebacterial DNA polymerase
11. Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius
12. Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7
13. Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1
14. Structure of the catalytic core of S. cerevisiae DNA polymerase η: Implications for translesion DNA synthesis
15. Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication
16. Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
17. Crystal structure of a bacteriophage T7 replication complex at 2.2 Å resolution
18. The mechanism of action of T7 DNA polymerase
19. Crystal structure of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis of nucleotide incorporation
20. Structure of the replicating complex of a Pol α family DNA polymerase
21. The polymerase subunit of DNA polymerase III of Escherichia coli. II. Purification of the α subunit, devoid of nuclease activities
22. DNA polymerase III holoenzyme: Structure and function of a chromosomal replicating machine
23. Identification of the ε-subunit of Escherichia coli DNA polymerase III holoenzyme as the dnaQ gene product: A fidelity subunit for DNA replication
24. Exonucleolytic proofreading
25. Processive replication is contingent on the exonuclease subunit of DNA polymerase III holoenzyme
26. umuDC-dnaQ interaction and its implications for cell cycle regulation and SOS mutagenesis in Escherichia coli
27. NMR solution structure of the θ subunit of DNA polymerase III from Escherichia coli
28. Two functional domains of the ε subunit of DNA polymerase III
29. Preliminary X-ray crystallographic and NMR studies on the exonuclease domain of the ε subunit of Escherichia coli DNA polymerase III
30. The C-terminal domain of DnaQ contains the polymerase binding site
31. Exonuclease X of Escherichia coli. A novel 3′-5′ DNase and DnaQ superfamily member involved in DNA repair
32. Eukaryotic DNA polymerase amino acid sequence required for 3′ → 5′ exonuclease activity
33. Evidence favouring the hypothesis of a conserved 3′-5′ exonuclease active site in DNA-dependent DNA polymerases
34. RNase T shares conserved sequence motifs with DNA proofreading exonucleases
35. Cocrystal structure of an editing complex of Klenow fragment with DNA
36. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism
37. The 3′-5′ exonuclease of DNA polymerase I of Escherichia coli: Contribution of each amino acid at the active site to the reaction
38. The 3′-5′ exonuclease site of DNA polymerase III from Gram-positive bacteria: Definition of a novel motif structure
39. Mutational analysis of the 3′→5′ proofreading exonuclease of Escherichia coli DNA polymerase III
40. The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains
41. Structure of Escherichia coli exonuclease I suggests how processivity is achieved
42. Model for the catalytic domain of the proofreading ε subunit of Escherichia coli DNA polymerase III based on NMR structural data
43. Kinetic mechanism of the 3′→5′ proofreading exonuclease of DNA polymerase III. Analysis by steady state and pre-steady state methods
44. Hydrolysis of the 5′-p-nitrophenyl ester of TMP by the proofreading exonuclease (ε) subunit of Escherichia coli DNA polymerase III
45. Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4
46. Processive proofreading is intrinsic to T4 DNA polymerase
47. Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction
48. Conformational coupling in DNA polymerase fidelity
49. Genetic and crystallographic studies of the 3′, 5′-exonucleolytic site of DNA polymerase I
50. Structural model for the editing decision of Escherichia coli DNA polymerase I
51. Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates
52. Structures of normal single-stranded DNA and deoxyribo-3′-S-phosphorothiolates bound to the 3′-5′ exonucleolytic active site of DNA polymerase I from Escherichia coli
53. Roles for the metal ion in reactions of coordinated substrates and in some metalloenzymes
54. Binuclear metallohydrolases
55. Enzyme-catalyzed phosphoryl transfer reactions
56. Stereochemical course of the 3′-5′ exonuclease activity of DNA polymerase I
57. Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate
58. Jack bean urease (EC 3.5.1.5). V. On the mechanism of action of urease on urea, formamide, acetamide, N-methylurea, and related compounds
59. Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis
60. 2+ ions reveals two divalent metals bound in the active site
61. A separate editing exonuclease for DNA replication: The ε subunit of Escherichia coli DNA polymerase III holoenzyme
62. Structure of DNA polymerase I Klenow fragment bound to duplex DNA
63. Specificity and enzymatic mechanism of the editing exonuclease of Escherichia coli DNA polymerase III
64. The CCP4 suite: Programs for protein crystallography
65. Crystallographic fast Fourier transforms
66. RSPS version 4.0: A semi-interactive vector-search program for solving heavy-atom derivatives
67. Maximum likelihood refinement of heavy atom parameters
68. Automated refinement of protein models
69. Improved methods for building protein models in electron density maps and the location of errors in these models
70. Crystallography and NMR system (CNS): A new software system for macromolecular structure determination
71. PROCHECK: A program to check the stereochemical quality of protein structures
72. Errors in protein structures
73. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
74. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
75. A solution for the best rotation to relate two sets of vectors
76. RIBBONS 2.0
77. Calculation of an OMIT map
78. Protein folding and associations: Insights from the interfacial and thermodynamic properties of the hydrocarbons