Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.

PubWeight™: 3.49‹?› | Rank: Top 1%

🔗 View Article (PMID 9016716)

Published in Structure on January 15, 1997

Authors

J R Kiefer1, C Mao, C J Hansen, S L Basehore, H H Hogrefe, J C Braman, L S Beese

Author Affiliations

1: Department of Biochemistry, Duke University Medical Centre, Durham, NC 27710, USA.

Articles citing this

MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr (2009) 53.36

Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc Natl Acad Sci U S A (2003) 3.67

The structural basis for the mutagenicity of O(6)-methyl-guanine lesions. Proc Natl Acad Sci U S A (2006) 3.01

Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius. Proc Natl Acad Sci U S A (1999) 2.19

Conformational transitions in DNA polymerase I revealed by single-molecule FRET. Proc Natl Acad Sci U S A (2009) 2.10

Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet. J Am Chem Soc (2008) 1.91

The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Structure (2010) 1.91

A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase. Proc Natl Acad Sci U S A (1998) 1.70

Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor. EMBO J (2005) 1.53

The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism. J Biol Chem (2011) 1.43

Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc Natl Acad Sci U S A (2011) 1.42

A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase. J Mol Biol (2006) 1.25

Lesion processing: high-fidelity versus lesion-bypass DNA polymerases. Trends Biochem Sci (2008) 1.24

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η. Biochemistry (2014) 1.23

Structural basis for the antiproliferative activity of the Tob-hCaf1 complex. J Biol Chem (2009) 1.16

A unique error signature for human DNA polymerase nu. DNA Repair (Amst) (2006) 1.16

Improving dideoxynucleotide-triphosphate utilisation by the hyper-thermophilic DNA polymerase from the archaeon Pyrococcus furiosus. Nucleic Acids Res (2000) 1.11

Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J Biol Chem (2012) 1.11

Mapping of ATP binding regions in poly(A) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases. Protein Sci (1999) 1.00

DNA polymerase preference determines PCR priming efficiency. BMC Biotechnol (2014) 0.99

Multiple functions of DNA polymerases. CRC Crit Rev Plant Sci (2007) 0.92

Chemical discrimination between dC and 5MedC via their hydroxylamine adducts. Nucleic Acids Res (2010) 0.91

Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template. Proc Natl Acad Sci U S A (2007) 0.91

Identification of conserved residues contributing to the activities of adenovirus DNA polymerase. J Virol (2000) 0.90

Unexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions. Nat Chem Biol (2013) 0.89

A 21-amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11-like and prefers manganese ion as the cofactor. Nucleic Acids Res (2004) 0.89

Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus. Biochemistry (2009) 0.87

Kinetic analysis of the unique error signature of human DNA polymerase ν. Biochemistry (2011) 0.86

Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. Nucleic Acids Res (2007) 0.85

A unique loop in the DNA-binding crevice of bacteriophage T7 DNA polymerase influences primer utilization. Proc Natl Acad Sci U S A (2000) 0.82

Phi29 DNA polymerase residues Tyr59, His61 and Phe69 of the highly conserved ExoII motif are essential for interaction with the terminal protein. Nucleic Acids Res (2002) 0.82

Molecular dynamics study of the opening mechanism for DNA polymerase I. PLoS Comput Biol (2014) 0.81

Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus. Proteins (2008) 0.80

Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase. Biochemistry (2009) 0.79

Nuclear DNA polymerase beta from Leishmania infantum. Cloning, molecular analysis and developmental regulation. Nucleic Acids Res (2001) 0.79

Modeling translocation dynamics of strand displacement DNA synthesis by DNA polymerase I. J Mol Model (2011) 0.76

The Closing Mechanism of DNA Polymerase I at Atomic Resolution. Structure (2015) 0.76

Optimal numbers of residues in linkers of DNA polymerase I, T7 primase and DNA polymerase IV. Sci Rep (2016) 0.75

The role of electrostatic interactions on klentaq1 insight for domain separation. Bioinform Biol Insights (2012) 0.75

Synthetic nucleotides as probes of DNA polymerase specificity. J Nucleic Acids (2012) 0.75

Translesion synthesis past guanine(C8)-thymine(N3) intrastrand cross-links catalyzed by selected A- and Y-family polymerases. Mol Biosyst (2016) 0.75

Enhancement of Polymerase Activity of the Large Fragment in DNA Polymerase I from Geobacillus stearothermophilus by Site-Directed Mutagenesis at the Active Site. Biomed Res Int (2016) 0.75

Mutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides. Nucleic Acids Res (2002) 0.75

Dynamics of DNA polymerase I (Klenow fragment) under external force. J Mol Model (2012) 0.75

Articles by these authors

PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res (1996) 6.04

Cystic fibrosis locus defined by a genetically linked polymorphic DNA marker. Science (1985) 5.81

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature (1998) 5.37

A polymorphic DNA marker linked to cystic fibrosis is located on chromosome 7. Nature (1985) 5.07

Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc Natl Acad Sci U S A (1988) 3.02

Identification of more than 500 RFLPs by screening random genomic clones. Am J Hum Genet (1988) 3.01

Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution. Science (1997) 2.34

Effect of stereochemistry on the anti-HIV activity of chiral thiourea compounds. Bioorg Med Chem (2004) 2.13

Involvement of yeast sphingolipids in the heat stress response of Saccharomyces cerevisiae. J Biol Chem (1997) 1.88

Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7. J Mol Biol (2000) 1.73

A closer look at water-related geologic activity on Mars. Science (2007) 1.71

Alternative RNA splicing generates transcripts encoding a thorax-specific isoform of Drosophila melanogaster myosin heavy chain. Mol Cell Biol (1986) 1.69

Identification of ISC1 (YER019w) as inositol phosphosphingolipid phospholipase C in Saccharomyces cerevisiae. J Biol Chem (2000) 1.65

Patient preferences regarding possible outcomes of lung resection: what outcomes should preoperative evaluations target? Chest (2000) 1.63

Search for supersymmetry using final states with one lepton, jets, and missing transverse momentum with the ATLAS detector in √s=7 TeV pp collisions. Phys Rev Lett (2011) 1.60

Carotid Doppler ultrasound criteria for internal carotid artery stenosis based on residual lumen diameter calculated from en bloc carotid endarterectomy specimens. Stroke (1996) 1.58

Sensitivity analyses including and excluding the HWE-violating studies are required for meta-analyses of genetic association studies. Breast Cancer Res Treat (2009) 1.56

Racial differences in patients' perceptions of debilitated health states. J Gen Intern Med (1999) 1.55

Essential role of the unfolded protein response regulator GRP78/BiP in protection from neuronal apoptosis. Cell Death Differ (2009) 1.55

The dust halo of Saturn's largest icy moon, Rhea. Science (2008) 1.52

Assembly of Borromean rings from DNA. Nature (1997) 1.51

Cloning the mouse homolog of the human cystic fibrosis transmembrane conductance regulator gene. Genomics (1991) 1.48

Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue. Biochemistry (1998) 1.46

Observation of a centrality-dependent dijet asymmetry in lead-lead collisions at sqrt[S(NN)] =2.76 TeV with the ATLAS detector at the LHC. Phys Rev Lett (2010) 1.41

Importance of time to reperfusion for 30-day and late survival and recovery of left ventricular function after primary angioplasty for acute myocardial infarction. J Am Coll Cardiol (1998) 1.39

Molecular analysis of G1B and G3A IFN gamma mutants reveals that defects in CIITA or RFX result in defective class II MHC and Ii gene induction. Immunity (1994) 1.39

Measurement of dijet azimuthal decorrelations in pp collisions at sqrt(s)=7  TeV. Phys Rev Lett (2011) 1.39

Comprehensive screening reveals strong and broadly directed human immunodeficiency virus type 1-specific CD8 responses in perinatally infected children. J Virol (2003) 1.38

Multimerization-cyclization of DNA fragments as a method of conformational analysis. Biophys J (2000) 1.35

Structure-based design of specific inhibitors of Janus kinase 3 as apoptosis-inducing antileukemic agents. Clin Cancer Res (1999) 1.32

Search for new particles in two-jet final states in 7 TeV proton-proton collisions with the ATLAS detector at the LHC. Phys Rev Lett (2010) 1.32

Cocrystal structure of protein farnesyltransferase complexed with a farnesyl diphosphate substrate. Biochemistry (1998) 1.29

Structure and specificity of T cell receptors expressed by potentially pathogenic anti-DNA autoantibody-inducing T cells in human lupus. J Clin Invest (1995) 1.26

The basis for K-Ras4B binding specificity to protein farnesyltransferase revealed by 2 A resolution ternary complex structures. Structure (2000) 1.26

The crystal structure of human protein farnesyltransferase reveals the basis for inhibition by CaaX tetrapeptides and their mimetics. Proc Natl Acad Sci U S A (2001) 1.25

DNA binding specificities of Spi-1/PU.1 and Spi-B transcription factors and identification of a Spi-1/Spi-B binding site in the c-fes/c-fps promoter. Oncogene (1995) 1.23

Expression of dominant-negative Ikaros isoforms in T-cell acute lymphoblastic leukemia. Clin Cancer Res (1999) 1.23

ART (protein product of agouti-related transcript) as an antagonist of MC-3 and MC-4 receptors. Biochem Biophys Res Commun (1997) 1.22

Identification of human antibody fragment clones specific for tetanus toxoid in a bacteriophage lambda immunoexpression library. Proc Natl Acad Sci U S A (1990) 1.20

Molecular determinants of ligand binding to the human melanocortin-4 receptor. Biochemistry (2000) 1.20

Cystic fibrosis transmembrane regulator regulates uptake of sphingoid base phosphates and lysophosphatidic acid: modulation of cellular activity of sphingosine 1-phosphate. J Biol Chem (2001) 1.19

Use of highly polymorphic DNA probes for genotypic analysis following bone marrow transplantation. Blood (1986) 1.18

Anti-HIV activity of aromatic and heterocyclic thiazolyl thiourea compounds. Bioorg Med Chem Lett (2001) 1.17

A new look at the saturn system: the voyager 2 images. Science (1982) 1.15

Phytosphingosine as a specific inhibitor of growth and nutrient import in Saccharomyces cerevisiae. J Biol Chem (2001) 1.12

Highly polymorphic RFLP probes as diagnostic tools. Cold Spring Harb Symp Quant Biol (1986) 1.09

Voyager 2 at neptune: imaging science results. Science (1989) 1.08

Two DNA polymerases: HIV reverse transcriptase and the Klenow fragment of Escherichia coli DNA polymerase I. Cold Spring Harb Symp Quant Biol (1993) 1.07

Localization of leptin binding domain in the leptin receptor. Mol Pharmacol (1998) 1.07

Outcomes of direct coronary angioplasty for acute myocardial infarction in candidates and non-candidates for thrombolytic therapy. Am J Cardiol (1991) 1.05

Cytokine gene expression in the MRL/lpr model of lupus nephritis. Kidney Int (1996) 1.02

Development of a novel continuous culture device for experimental evolution of bacterial populations. Appl Microbiol Biotechnol (2007) 1.02

Physicians' opinions of the accuracy, accessibility, and frequency of use of ten sources of new drug information. South Med J (1986) 1.01

Analysis of transcripts that are differentially expressed in three sectors of the rice root system under water deficit. Mol Genet Genomics (2004) 1.00

Adenovirus 36 seropositivity is strongly associated with race and gender, but not obesity, among US military personnel. Int J Obes (Lond) (2009) 1.00

Molecular and enzymatic profiles of mammalian DNA methyltransferases: structures and targets for drugs. Curr Med Chem (2010) 0.99

Sequence dependence of branch migratory minima. J Mol Biol (1998) 0.99

Transcription factor STAT5A is a substrate of Bruton's tyrosine kinase in B cells. J Biol Chem (2001) 0.98

Ydc1p ceramidase triggers organelle fragmentation, apoptosis and accelerated ageing in yeast. Cell Mol Life Sci (2008) 0.97

Contrast visual testing in neurovisual diagnosis. Neurology (1987) 0.96

Spleen tyrosine kinase (Syk) deficiency in childhood pro-B cell acute lymphoblastic leukemia. Oncogene (2001) 0.96

Polymorphisms of the endothelial nitric oxide synthase gene - no consistent association with myocardial infarction in the ECTIM study. Eur J Clin Invest (1999) 0.95

Structure-based design of novel dihydroalkoxybenzyloxopyrimidine derivatives as potent nonnucleoside inhibitors of the human immunodeficiency virus reverse transcriptase. Antimicrob Agents Chemother (1998) 0.95

Molecular interaction of Agouti protein and Agouti-related protein with human melanocortin receptors. Biochemistry (1999) 0.95

Emx1-specific expression of foreign genes using "knock-in" approach. Biochem Biophys Res Commun (2000) 0.93

Active center cleft residues of pokeweed antiviral protein mediate its high-affinity binding to the ribosomal protein L3. Biochemistry (2001) 0.93

A method for the site-directed mono- and multi-mutagenesis of double-stranded DNA. Gene (1993) 0.93

DNA polymerases from hyperthermophiles. Methods Enzymol (2001) 0.92

Encounter with saturn: voyager 1 imaging science results. Science (1981) 0.92

Residents' leadership styles and effectiveness as perceived by nurses. J Med Educ (1986) 0.92

X-ray crystallographic analysis of pokeweed antiviral protein-II after reductive methylation of lysine residues. Biochem Biophys Res Commun (2000) 0.91

Proteinase inhibitor 9, an inhibitor of granzyme B-mediated apoptosis, is a primary estrogen-inducible gene in human liver cells. J Biol Chem (2000) 0.89

Binding interactions between the active center cleft of recombinant pokeweed antiviral protein and the alpha-sarcin/ricin stem loop of ribosomal RNA. J Biol Chem (2001) 0.89

Importance of a patent infarct-related artery for hospital and late survival after direct coronary angioplasty for acute myocardial infarction. Am J Cardiol (1992) 0.89

Atomic structure at 2.5 A resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice. FEBS Lett (1995) 0.89

Loss of PTEN expression predicts resistance to EGFR-targeted monoclonal antibodies in patients with metastatic colorectal cancer. Br J Cancer (2010) 0.89

Estrogen receptor-KRAB chimeras are potent ligand-dependent repressors of estrogen-regulated gene expression. J Biol Chem (2000) 0.89

No braiding of Holliday junctions in positively supercoiled DNA molecules. J Mol Biol (1999) 0.88

Importance of infarct-related artery patency for recovery of left ventricular function and late survival after primary angioplasty for acute myocardial infarction. J Am Coll Cardiol (1996) 0.87

Microvascular autologous submandibular gland transfer in severe cases of keratoconjunctivitis sicca. Int J Oral Maxillofac Surg (2004) 0.85

Types of female partners reported by black men who have sex with men and women (MSMW) and associations with intercourse frequency, unprotected sex and HIV and STI prevalence. AIDS Behav (2014) 0.82

Single-dose pharmacokinetics and tolerability of alendronate 35- and 70-milligram tablets in children and adolescents with osteogenesis imperfecta type I. J Clin Endocrinol Metab (2005) 0.82

Kinetic analysis of zinc ligand mutants of mammalian protein farnesyltransferase. Biochemistry (1998) 0.82

Conversion of Tyr361 beta to Leu in mammalian protein farnesyltransferase impairs product release but not substrate recognition. Biochemistry (2000) 0.81

N'-[2-(2-thiophene)ethyl]-N'-[2-(5-bromopyridyl)] thiourea as a potent inhibitor of NNI-resistant and multidrug-resistant human immunodeficiency virus-1. Bioorg Med Chem Lett (1999) 0.81

Rational design and synthesis of phenethyl-5-bromopyridyl thiourea derivatives as potent non-nucleoside inhibitors of HIV reserve transcriptase. Bioorg Med Chem (1998) 0.81

Search for diphoton events with large missing transverse energy in 7 TeV proton-proton collisions with the ATLAS detector. Phys Rev Lett (2011) 0.81

In vitro role of IL-1 in heightened IgG, anti-DNA, and nephritogenic idiotype production by B cells derived from the murine MRL/lpr lupus model. Clin Immunol Immunopathol (1994) 0.81

Photo-cross-linking of rabbit skeletal troponin I deletion mutants with troponin C and its thiol mutants: the inhibitory region enhances binding of troponin I fragments to troponin C. Biochemistry (1996) 0.80

Pathogenic autoantibody-inducing gamma/delta T helper cells from patients with lupus nephritis express unusual T cell receptors. Clin Immunol Immunopathol (1992) 0.80

Jagged-1-HES-1 signaling inhibits the differentiation of TH17 cells via ROR gammat. J Biol Regul Homeost Agents (2013) 0.80

Structure-based design of novel anticancer agents. Curr Cancer Drug Targets (2001) 0.80

IL-10 promoter SNPs and susceptibility to leprosy in ethnic groups from southwest China. Genet Mol Res (2013) 0.79

Two dimensions and two States in DNA nanotechnology. J Biomol Struct Dyn (2000) 0.79

Small-sample total RNA purification: laser capture microdissection and cultured cell applications. Biotechniques (2001) 0.79

Emergency coronary angioplasty for acute myocardial infarction. Results from a community hospital. Arch Intern Med (1987) 0.79