scholarly journals Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding

2021 ◽  
Author(s):  
Michael Taschner ◽  
Jérôme Basquin ◽  
Barbara Steigenberger ◽  
Ingmar B Schäfer ◽  
Young‐Min Soh ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Dna Substrate

scholarly journals Characterization of DNA Substrate Binding to the Phosphatase Domain of the DNA Repair Enzyme Polynucleotide Kinase/Phosphatase

Biochemistry ◽  
2017 ◽  
Vol 56 (12) ◽  
pp. 1737-1745 ◽  
Author(s):  
Zahra Havali-Shahriari ◽  
Michael Weinfeld ◽  
J. N. Mark Glover
Keyword(s):  
Dna Repair ◽  
Substrate Binding ◽  
Repair Enzyme ◽  
Phosphatase Domain ◽  
Polynucleotide Kinase ◽  
Dna Substrate

scholarly journals Insights into the role of Val45 and Gln182 of Escherichia coli MutY in DNA substrate binding and specificity

2009 ◽  
Vol 10 (1) ◽  
pp. 19 ◽  
Author(s):  
Po-Wen Chang ◽  
Amrita Madabushi ◽  
A-Lien Lu
Keyword(s):  
Escherichia Coli ◽  
Substrate Binding ◽  
Dna Substrate

scholarly journals Structural characterization of the virulence factor nuclease A fromStreptococcus agalactiae

2014 ◽  
Vol 70 (11) ◽  
pp. 2937-2949 ◽  
Author(s):  
Andrea F. Moon ◽  
Philippe Gaudu ◽  
Lars C. Pedersen
Keyword(s):  
Virulence Factor ◽  
Substrate Binding ◽  
Nuclease Activity ◽  
Structure Based Drug Design ◽  
X Ray Crystallography ◽  
High Resolution Structure ◽  
Group B ◽  
Increased Activity ◽  
Dna Substrate

The group B pathogenStreptococcus agalactiaecommonly populates the human gut and urogenital tract, and is a major cause of infection-based mortality in neonatal infants and in elderly or immunocompromised adults. Nuclease A (GBS_NucA), a secreted DNA/RNA nuclease, serves as a virulence factor forS. agalactiae, facilitating bacterial evasion of the human innate immune response. GBS_NucA efficiently degrades the DNA matrix component of neutrophil extracellular traps (NETs), which attempt to kill and clear invading bacteria during the early stages of infection. In order to better understand the mechanisms of DNA substrate binding and catalysis of GBS_NucA, the high-resolution structure of a catalytically inactive mutant (H148G) was solved by X-ray crystallography. Several mutants on the surface of GBS_NucA which might influence DNA substrate binding and catalysis were generated and evaluated using an imidazole chemical rescue technique. While several of these mutants severely inhibited nuclease activity, two mutants (K146R and Q183A) exhibited significantly increased activity. These structural and biochemical studies have greatly increased our understanding of the mechanism of action of GBS_NucA in bacterial virulence and may serve as a foundation for the structure-based drug design of antibacterial compounds targeted toS. agalactiae.

scholarly journals Thermodynamics of the DNA Repair Process by Endonuclease VIII

Acta Naturae ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 29-37 ◽  
Author(s):  
O. A. Kladova ◽  
N. A. Kuznetsov ◽  
O. S. Fedorova
Keyword(s):  
Activation Enthalpy ◽  
Substrate Binding ◽  
Repair Process ◽  
Molecular Processes ◽  
Substrate Interaction ◽  
Enzyme Substrate ◽  
Different Temperatures ◽  
Enthalpy And Entropy ◽  
Transition Complex ◽  
Dna Substrate

In the present work, a thermodynamic analysis of the interaction between endonuclease VIII (Endo VIII) and model DNA substrates containing damaged nucleotides, such as 5,6-dihydrouridine and 2-hydroxymethyl-3-hydroxytetrahydrofuran (F-site), was performed. The changes in the fluorescence intensity of the 1,3-diaza-2-oxophenoxazine (tCO) residue located in the complementary chain opposite to the specific site were recorded in the course of the enzyme-substrate interaction. The kinetics was analyzed by the stopped-flow method at different temperatures. The changes of standard Gibbs free energy, enthalpy, and entropy of sequential steps of DNA substrate binding, as well as activation enthalpy and entropy for the transition complex formation of the catalytic stage, were calculated. The comparison of the kinetic and thermodynamic data characterizing the conformational transitions of enzyme and DNA in the course of their interaction made it possible to specify the nature of the molecular processes occurring at the stages of substrate binding, recognition of the damaged base, and its removal from DNA.

scholarly journals Newly Discovered Archaebacterial Flap Endonucleases Show a Structure-Specific Mechanism for DNA Substrate Binding and Catalysis Resembling Human Flap Endonuclease-1

1998 ◽  
Vol 273 (42) ◽  
pp. 27154-27161 ◽  
Author(s):  
David J. Hosfield ◽  
Geoffrey Frank ◽  
Yehua Weng ◽  
John A. Tainer ◽  
Binghui Shen
Keyword(s):  
Substrate Binding ◽  
Specific Mechanism ◽  
Flap Endonuclease 1 ◽  
Dna Substrate

scholarly journals Defining the DNA Substrate Binding Sites on HIV-1 Integrase

2009 ◽  
Vol 385 (2) ◽  
pp. 568-579 ◽  
Author(s):  
James Dolan ◽  
Aiping Chen ◽  
Irene T. Weber ◽  
Robert W. Harrison ◽  
Jonathan Leis
Keyword(s):  
Binding Sites ◽  
Substrate Binding ◽  
Substrate Binding Sites ◽  
Dna Substrate ◽  
Hiv 1

Fibronexus-Like Adhesion Sites are Present at the Invasive Zones of Human Epidermoid Carcinomas

1982 ◽  
Vol 40 ◽  
pp. 106-109
Author(s):  
Irwin I. Singer
Keyword(s):  
Cell Cycle ◽  
Serum Concentration ◽  
Substrate Binding ◽  
High Serum ◽  
Adhesion Sites ◽  
Substrate Adhesion ◽  
Focal Contacts ◽  
Adhesion Complex ◽  
Low Serum

Our previous results indicate that two types of fibronectin-cytoskeletal associations may be formed at the fibroblast surface: dorsal matrixbinding fibronexuses generated in high serum (5% FBS) cultures, and ventral substrate-adhering units formed in low serum (0.3% FBS) cultures. The substrate-adhering fibronexus consists of at least vinculin (VN) and actin in its cytoplasmic leg, and fibronectin (FN) as one of its major extracellular components. This substrate-adhesion complex is localized in focal contacts, the sites of closest substratum approach visualized with interference reflection microscopy, which appear to be the major points of cell-tosubstrate adhesion. In fibroblasts, the latter substrate-binding complex is characteristic of cultures that are arrested at the G1 phase of the cell cycle due to the low serum concentration in their medium. These arrested fibroblasts are very well spread, flattened, and immobile.

Contributions of the substrate-binding arginine residues to maleate-induced closure of the active site of Escherichia coli aspartate aminotransferase

2001 ◽  
Vol 268 (6) ◽  
pp. 1640-1645
Author(s):  
Annelise Matharu ◽  
Hideyuki Hayashi ◽  
Hiroyuki Kagamiyama ◽  
Bruno Maras ◽  
Robert A. John
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Aspartate Aminotransferase ◽  
Substrate Binding ◽  
Arginine Residues
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