Structure of the replicating complex of a pol α family DNA polymerase

Cell

Volumn 105, Issue 5, 2001, Pages 657-667

  Franklin, Matthew C ^a   Wang, Jimin ^a   Steitz, Thomas A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; PRIMER DNA;

ARTICLE; CRYSTAL STRUCTURE; DNA STRUCTURE; DNA TEMPLATE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME MECHANISM; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE;

EID: 0035369086     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(01)00367-1     Document Type: Article

References (71)

1. A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides
2. Sequence analysis of the 17,166 base-pair EcoRI fragment C of B95-8 Epstein-Barr virus
3. Structure of DNA polymerase I Klenow fragment bound to duplex DNA
4. Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate
5. The carboxyl terminus of the bacteriophage T4 DNA polymerase is required for holoenzyme complex formation
6. Calculation of an OMIT map
7. Primer terminus stabilization at the phi 29 DNA polymerase active site. Mutational analysis of conserved motif KXY
8. A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type phi29 DNA polymerase
9. Compilation, alignment, and phylogenetic relationships of DNA polymerases
10. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes
11. The free R value: A novel statistical quantity for assessing the accuracy of crystal structures
12. Crystallography & NMR system: A new software suite for macromolecular structure determination
13. Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4
14. Mutational analysis of the human DNA polymerase alpha. The most conserved region in alpha-like DNA polymerases is involved in metal-specific catalysis
15. DNA substrate structural requirements for the exonuclease and polymerase activities of procaryotic and phage DNA polymerases
16. Kinetic mechanism of DNA polymerase I (Klenow fragment): Identification of a second conformational change and evaluation of the internal equilibrium constant
17. An attempt to unify the structure of polymerases
18. Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction
19. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
20. An open and closed case for all polymerases
21. A constant rate of spontaneous mutation in DNA-based microbes
22. Retention of replication fidelity by a DNA polymerase functioning in a distantly related environment
23. Structure of Taq polymerase with DNA at the polymerase active site
24. Physiological studies of conditional lethal mutants of bacteriophage T4D
25. The nucleotide analog 2-aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase
26. Conferring RNA polymerase activity to a DNA polymerase: A single residue in reverse transcriptase controls substrate selection
27. Determinants of nucleotide sugar recognition in an archaeon DNA polymerase
28. Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius
29. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance
30. Genetic mapping of the amino-terminal domain of bacteriophage T4 DNA polymerase
31. Structural features and hydration of a dodecamer duplex containing two C.A mispairs
32. The structure of guanosine-thymidine mismatches in B-DNA at 2.5 Å resolution
33. Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 Å resolution shows bent DNA
34. Structure of an RNA internal loop consisting of tandem C-A+ base pairs
35. Conformational coupling in DNA polymerase fidelity
36. Improved methods for building protein models in electron density maps and the location of errors in these models
37. DNA polymerase of the T4-related bacteriophages
38. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
39. Replication of non-hydrogen bonded bases by DNA polymerases: A mechanism for steric matching
40. Kinetic mechanism of DNA polymerase I (Klenow)
41. Procheck: A program to check the stereochemical quality of protein structures
42. 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
43. Isolation, characterization, and kinetic properties of truncated forms of T4 DNA polymerase that exhibit 3′-5′ exonuclease activity
44. Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment)
45. AMoRe: An automated package for molecular replacement
46. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
47. Processing of x-ray diffraction data collected in oscillation mode
48. Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs
49. Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant
50. Nucleotide-sequence-specific and non-specific interactions of T4 DNA polymerase with its own mRNA
51. Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP
52. Improved Fourier coefficients for maps using phases from partial structures with errors
53. Locations of amino acid substitutions in bacteriophage T4 tsL56 DNA polymerase predict an N-terminal exonuclease domain
54. Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement
55. Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7
56. A novel kinetic analysis to calculate nucleotide affinity of proofreading DNA polymerases. Application to phi 29 DNA polymerase fidelity mutants
57. Role of the first aspartate residue of the "YxDTDS" motif of phi29 DNA polymerase as a metal ligand during both TP-primed and DNA-primed DNA synthesis
58. Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
59. Smart: A web-based tool for the study of genetically mobile domains
60. Sequence-specific recognition of double helical nucleic acids by proteins
61. Building a replisome from interacting pieces: Sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex
62. DNA- and RNA-dependent DNA polymerases
63. Dynamics of bacteriophage T4 DNA polymerase function: Identification of amino acid residues that affect switching between polymerase and 3′→ 5′ exonuclease activities
64. Autogenous translational operator recognized by bacteriophage T4 DNA polymerase
65. Modular organization of T4 DNA polymerase. Evidence from phylogenetics
66. Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69
67. An induced-fit kinetic mechanism for DNA replication fidelity: Direct measurement by single-turnover kinetics
68. Kinetic characterization of a bacteriophage T4 antimutator DNA polymerase
69. Steady-state kinetic characterization of RB69 DNA polymerase mutants that affect dNTP incorporation
70. Crystal structure of an archaebacterial DNA polymerase