scholarly journals A structural study of TatD from Staphylococcus aureus elucidates a putative DNA-binding mode of a Mg2+-dependent nuclease

IUCrJ ◽  
2020 ◽  
Vol 7 (3) ◽  
pp. 509-521
Author(s):  
Kyu-Yeon Lee ◽  
Seung-Ho Cheon ◽  
Dong-Gyun Kim ◽  
Sang Jae Lee ◽  
Bong-Jin Lee
Keyword(s):  
Crystal Structure ◽  
Staphylococcus Aureus ◽  
Dna Binding ◽  
Catalytic Mechanism ◽  
Nuclease Activity ◽  
Binding Mode ◽  
Functional Study ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Key Residues

TatD has been thoroughly investigated as a DNA-repair enzyme and an apoptotic nuclease, and still-unknown TatD-related DNases are considered to play crucial cellular roles. However, studies of TatD from Gram-positive bacteria have been hindered by an absence of atomic detail and the resulting inability to determine function from structure. In this study, an X-ray crystal structure of SAV0491, which is the TatD enzyme from the Gram-positive bacterium Staphylococcus aureus (SaTatD), is reported at a high resolution of 1.85 Å with a detailed atomic description. Although SaTatD has the common TIM-barrel fold shared by most TatD-related homologs, and PDB entry 2gzx shares 100% sequence identity with SAV0491, the crystal structure of SaTatD revealed a unique binding mode of two phosphates interacting with two Ni2+ ions. Through a functional study, it was verified that SaTatD has Mg2+-dependent nuclease activity as a DNase and an RNase. In addition, structural comparison with TatD homologs and the identification of key residues contributing to the binding mode of Ni2+ ions and phosphates allowed mutational studies to be performed that revealed the catalytic mechanism of SaTatD. Among the key residues composing the active site, the acidic residues Glu92 and Glu202 had a critical impact on catalysis by SaTatD. Furthermore, based on the binding mode of the two phosphates and structural insights, a putative DNA-binding mode of SaTatD was proposed using in silico docking. Overall, these findings may serve as a good basis for understanding the relationship between the structure and function of TatD proteins from Gram-positive bacteria and may provide critical insights into the DNA-binding mode of SaTatD.

DNA Binding Ligands with Excellent Antibiotic Potency Against Drug-Resistant Gram-Positive Bacteria.

ChemInform ◽  
2003 ◽  
Vol 34 (6) ◽  
Author(s):  
Roland W. Buerli ◽  
Yigong Ge ◽  
Sarah White ◽  
Eldon E. Baird ◽  
Sofia M. Touami ◽  
...  
Keyword(s):  
Dna Binding ◽  
Drug Resistant ◽  
Gram Positive ◽  
Gram Positive Bacteria

scholarly journals In Vitro and In Vivo Activities of DA-7867, a New Oxazolidinone, against Aerobic Gram-Positive Bacteria

2005 ◽  
Vol 49 (6) ◽  
pp. 2498-2500 ◽  
Author(s):  
Eun Jeong Yoon ◽  
Yeong Woo Jo ◽  
Sung Hak Choi ◽  
Tae Ho Lee ◽  
Jae Keol Rhee ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Streptococcus Pneumoniae ◽  
Gram Positive ◽  
Methicillin Resistant ◽  
Gram Positive Bacteria ◽  
Vancomycin Resistant Enterococci ◽  
Infection Models ◽  
Vancomycin Resistant

ABSTRACT In vitro and in vivo activities of DA-7867 were assessed against methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, and penicillin-resistant Streptococcus pneumoniae. All isolates were inhibited by DA-7867 at ≤0.78 μg/ml, a four-times-lower concentration than that of inhibition by linezolid. For murine infection models, DA-7867 also exhibited greater efficacy than linezolid against all isolates tested.

scholarly journals Antimicrobial Activity of Gardenia jasminoides Callus and Crude Leaf Extracts for some Organic Solvents against some Pathogenic Bacteria and Yeasts

2014 ◽  
Vol 8 (3) ◽  
pp. 40-45
Author(s):  
Zina Hashem Shehab ◽  
Huda Suhail Abid ◽  
Sumaya Fadhil Hamad ◽  
Sara Haitham
Keyword(s):  
Staphylococcus Aureus ◽  
Candida Albicans ◽  
Pathogenic Bacteria ◽  
Saccharomyces Boulardii ◽  
Gram Negative Bacteria ◽  
Proteus Vulgaris ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Gardenia Jasminoides

The study was conducted to evaluate the inhibitory activity of methanol extract of Gardenia jasminoides leaves compared with leaf crude extracts for some organic solvents namely Methanol, Ethanol, Petroleum ether, Asetone and Chloroform on growth of some pathogenic bacteria and yeast, which included four gram positive isolates Staphylococcus aureus, Enterococcus faecalis, Streptococcus pyogenes and Bacillus cereus and gram negative isolates Escherichia coli, Salmonella typhi, Proteus vulgaris and Pseudomonas aeruginosa and some yeasts Candida albicans and Saccharomyces boulardii, by using well diffusion method. The inhibitory activity of extracts in the tested bacterial strains and yeasts was varied according to the type of extracting solvents and are tested microorganisms. The methanol callus extract which grown on Murashige and Skoog (MS) media by using (Naphthalen acitic acid) NAA and (Benzyle adenine) BA as growth regulator highly effective as compared to the other extracts as for inhibition of three gram positive bacteria and three gram negative bacteria,which include Staphylococcus aureus and, Proteus vulgaris, followed by acetone and ethanolic extracts which include two gram positive bacteria and two gram negative bacteria. All extracts had highly effect in growth of Candida albicans while all crude extracts didn’t show any sensitivity against Saccharomyces boulardii, and when we’d done (High Performance Liquid Chromatography) HPLC test for detection of some active compound we found Quinic acid, Iridiods glycosides and Crocin which its rate in fresh callus was higher than fresh leaves.

scholarly journals Activities of Oxadiazole Antibacterials against Staphylococcus aureus and Other Gram-Positive Bacteria

2018 ◽  
Vol 62 (8) ◽  
Author(s):  
Sara Ceballos ◽  
Choon Kim ◽  
Derong Ding ◽  
Shahriar Mobashery ◽  
Mayland Chang ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Gram Positive ◽  
Methicillin Resistant ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Vancomycin Resistant Enterococci ◽  
Vancomycin Resistant ◽  
Mrsa Strains

ABSTRACT The activities of four oxadiazoles were investigated with 210 methicillin-resistant Staphylococcus aureus (MRSA) strains. MIC50 and MIC90 values of 1 to 2 and 4 μg/ml, respectively, were observed. We also evaluated the activity of oxadiazole ND-421 against other staphylococci and enterococci and in the presence of oxacillin for selected MRSA strains. The MIC for ND-421 is lowered severalfold in combination with oxacillin, as they synergize. The MIC90 of ND-421 against vancomycin-resistant enterococci is ≤1 μg/ml.

Covalent Sortase A Inhibitor ML346 Prevents Staphylococcus aureus Infection of Galleria mellonella

2021 ◽  
Author(s):  
Xiang-Na Guan ◽  
Tao Zhang ◽  
Teng Yang ◽  
Ze Dong ◽  
Song Yang ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Galleria Mellonella ◽  
Surface Proteins ◽  
Sortase A ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Aureus Infection ◽  
Cell Wall Peptidoglycan

The housekeeping sortase A (SrtA), a membrane-associated cysteine transpeptidase, is responsible for anchoring surface proteins to the cell wall peptidoglycan in Gram-positive bacteria. This process is essential for the regulation...

Structural and functional studies of SAV1707 from Staphylococcus aureus elucidate its distinct metal-dependent activity and a crucial residue for catalysis

2021 ◽  
Vol 77 (5) ◽  
pp. 587-598
Author(s):  
Dong-Gyun Kim ◽  
Kyu-Yeon Lee ◽  
Sang Jae Lee ◽  
Seung-Ho Cheon ◽  
Yuri Choi ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Metal Binding ◽  
Binding Mode ◽  
Structure And Function ◽  
Functional Study ◽  
Functional Studies ◽  
Dependent Endonuclease ◽  
Metal Selectivity ◽  
Metal Binding Domain ◽  
And Function

The metallo-β-lactamase fold is the most abundant metal-binding domain found in two major kingdoms: bacteria and archaea. Despite the rapid growth in genomic information, most of these enzymes, which may play critical roles in cellular metabolism, remain uncharacterized in terms of structure and function. In this study, X-ray crystal structures of SAV1707, a hypothetical metalloenzyme from Staphylococcus aureus, and its complex with cAMP are reported at high resolutions of 2.05 and 1.55 Å, respectively, with a detailed atomic description. Through a functional study, it was verified that SAV1707 has Ni2+-dependent phosphodiesterase activity and Mn2+-dependent endonuclease activity, revealing a different metal selectivity depending on the reaction. In addition, the crystal structure of cAMP-bound SAV1707 shows a unique snapshot of cAMP that reveals the binding mode of the intermediate, and a key residue Phe511 that forms π–π interactions with cAMP was verified as contributing to substrate recognition by functional studies of its mutant. Overall, these findings characterized the relationship between the structure and function of SAV1707 and may provide further understanding of metalloenzymes possessing the metallo-β-lactamase fold.

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