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1.
《Journal of molecular biology》2021,433(15):167097
DNA glycosylases remove damaged or modified nucleobases by cleaving the N-glycosyl bond and the correct nucleotide is restored through subsequent base excision repair. In addition to excising threatening lesions, DNA glycosylases contribute to epigenetic regulation by mediating DNA demethylation and perform other important functions. However, the catalytic mechanism remains poorly defined for many glycosylases, including MBD4 (methyl-CpG binding domain IV), a member of the helix-hairpin-helix (HhH) superfamily. MBD4 excises thymine from G·T mispairs, suppressing mutations caused by deamination of 5-methylcytosine, and it removes uracil and modified uracils (e.g., 5-hydroxymethyluracil) mispaired with guanine. To investigate the mechanism of MBD4 we solved high-resolution structures of enzyme-DNA complexes at three stages of catalysis. Using a non-cleavable substrate analog, 2′-deoxy-pseudouridine, we determined the first structure of an enzyme-substrate complex for wild-type MBD4, which confirms interactions that mediate lesion recognition and suggests that a catalytic Asp, highly conserved in HhH enzymes, binds the putative nucleophilic water molecule and stabilizes the transition state. Observation that mutating the Asp (to Gly) reduces activity by 2700-fold indicates an important role in catalysis, but probably not one as the nucleophile in a double-displacement reaction, as previously suggested. Consistent with direct-displacement hydrolysis, a structure of the enzyme-product complex indicates a reaction leading to inversion of configuration. A structure with DNA containing 1-azadeoxyribose models a potential oxacarbenium-ion intermediate and suggests the Asp could facilitate migration of the electrophile towards the nucleophilic water. Finally, the structures provide detailed snapshots of the HhH motif, informing how these ubiquitous metal-binding elements mediate DNA binding. 相似文献
2.
The biologically important pyridoxinato(1−) ligand (anionic vitamin B6) shows the rare phenolate-hydroxymethyl chelation plus bridging mode through the pyridine-nitrogen atom towards zinc(II) to give the one-dimensional (1D) coordination polymer {(acetato-κO)-aqua-μ-[2-methyl-3-oxy-4,5-di(hydroxymethyl)pyridine-κN:O,O′]zinc(II)}·monohydrate with polar packing of adjacent chains along the polar c axis (in space group Pc) through strong inter-chain hydrogen bonding. 相似文献
3.
《Current biology : CB》2020,30(18):3544-3555.e6
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Summary The developing pigment strand of rice (Oryza sativa L.) was studied by conventional electron microscopy and also by use of thick sections post-fixed with zinc iodide and osmium (ZIO).When the rice caryopsis achieves maximum length, a suberised adcrusting wall layer is laid down over the original primary walls of the pigment strand. Concomitant with suberin deposition a proliferation of tubular endoplasmic reticulum occurs in the cytoplasm giving rise to numerous interconnected vesicles which bear ribosomes. The vesicles in the general cytoplasm retain their ribosomes while those close to the wall become smooth and contain an electron-opaque granular material which is eventually deposited to the outside of the plasmalemma. This granular material may be the precursor(s) from which suberin is polymerised. The suberised wall attains about six times the width of the original primary wall and plasmodesmata, which traverse both primary wall and suberised wall layers, become greatly elongated.Lipid bodies increase in both size and frequency during development, eventually coalescing to form a complete plug across the pigment strand and occluding the symplast of this tissue. The significance of these ultrastructural observations is discussed in relation to the previously demonstrated role of the pigment strand as a translocation pathway for water and assimilates during grain filling.Abbreviations ER
endoplasmic reticulum
- ZIO
zinc iodide-osmium fixation 相似文献
6.
Margarita Burguera-Pascu Alberto Rodríguez-Archilla Pilar Baca 《Journal of trace elements in medicine and biology》2007,21(2):92-101
The antimicrobial efficacy of zinc (Zn) salts (sulfate and acetate) against Streptococcus mutans (S. mutans) present in the oral cavity was tested in this study. The substantivity of Zn salts was assessed by determining the concentration of Zn in whole, unstimulated saliva and by measuring the magnitude of suppression of salivary S. mutans, 2h after rinsing. The concentration of Zn was measured by atomic absorption spectrometry (AAS) with electrothermal atomization (ET AAS) in saliva sampled before (basal) and 24h after mouth rinsing with different concentrations of Zn (0.1%, 0.5% and 1%) administrated as sulfate and acetate. The estimation of Zn levels in samples collected 30, 60, 90 and 120 min after rinsing was carried out by AAS with flame atomization (FAAS). Immediately after rinsing, the concentration of Zn in saliva sharply increased with respect to the baseline values (0.055+/-0.017 mg/L), followed by a sustained decrease, probably due to clearance of salivary flow or swallowing during sampling. A significant reduction (>87%) in the total mean S. mutans counts was found 2h after rinsing either with sulfate or acetate solutions, as evidence of the high substantivity and effectiveness of the Zn salts tested. A statistically significant inverse relationship (p<0.001 and the Pearson correlation coefficients between -34% and -50%) was found between Zn levels and the respective pH values measured in the samples collected 60 and 120 min after rinsing, sustaining the theory of bacterial glycolysis inhibition. 相似文献
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Lyn D. Olson Carolyn A. Renshaw Shlomo Rottem Jila H. Boal 《FEMS microbiology letters》1993,108(1):47-51
Abstract Electrofusion of protoplasts of two mutant strains of Hansenula polymorpha resulted in high fusion and hybrid yields when the calcium ions present in the conventional fusion medium replaced by zinc ions. The optimal fusion conditions were an alignment field of 0.4 kV cm−1 strength and 2 MHz frequency for 30 s, followed by two consecutive pulses of 12 kV cm−1 strength and 15 μs duration. With 0.05–0.1 mM zinc ions in the fusion medium an average clone number of 104 –105 clones per 108 input cells was reached. The presence of about 0.6 mM magnesium ions in the zinc fusion medium was essential. 相似文献
9.
Blood was obtained from 564 11-yr-old children who had participated since birth in a multidisciplinary health and development
study. Serum zinc concentration did not differ between the boys and the girls (mean±SD: 91=17 μg/100 mL,n=453). Five-6% of serum zinc values were low; although there was a weak correlation with height, none of the boys with low
values were below the 10th percentile for height for this group. Serum copper concentration (112±24 μg/100 mL,n=454) was unrelated to sex, height, weight, body mass index, socioeconomic status (SES), or iron status. Blood selenium concentration
(49±10 ng/mL,n=564) was lower than previously reported for Dunedin children; it was higher in children in the lower SES categories. The
data represent normal values for healthy, 11-yr-old NZ children. 相似文献
10.
The effect of pretransplant inoculation with VA mycorrhizal fungi on the subsequent growth of leeks in the field 总被引:1,自引:1,他引:0
Summary Leek plants were preinoculated with a mixed inoculum ofGlomus caledonium, Glomus fasciculatum andGlomus sp., and transplanted to Dazomet disinfected and untreated field plots of moderate P deficiency. Successive harvests were
made until 99 days after transplanting. Preinoculated leeks attained marketable weights 25 days earlier than uninoculated
leeks from untreated soil and their final dry matter yields were 5.7 and 1.5 times as high as those of uninoculated leeks
from disinfected and untreated soil, respectively. Phosphorus concentration in preinoculated leeks remained highest for at
least 22 and 75 days after transplanting in untreated and disinfected soil, respectively. Preinoculation had a similar, although
smaller, influence on Cu and Zn concentrations. Infection levels produced by introduced and indigenous VA endophytes in leeks
reached plateaus of 90% and 40%, respectively, 47 days after transplanting. It is concluded that VAM is essential to leeks
grown in moderately P deficient soils, and the potential for inoculating seedlings in commercial leek production is discussed. 相似文献