scholarly journals Structural Analysis of an L-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Liqiong Liu ◽  
Susu Jiang ◽  
Mai Xing ◽  
Chao Chen ◽  
Chongde Lai ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Change ◽  
Molecular Mechanism ◽  
Sulfur Atom ◽  
Nucleophilic Attack ◽  
Nonbridging Oxygen ◽  
Long Distance ◽  
Cysteine Desulfurase ◽  
Modification System ◽  
Pt Modification

ABSTRACT DNA phosphorothioate (PT) modification, in which the nonbridging oxygen in the sugar-phosphate backbone is substituted by sulfur, is catalyzed by DndABCDE or SspABCD in a double-stranded or single-stranded manner, respectively. In Dnd and Ssp systems, mobilization of sulfur in PT formation starts with the activation of the sulfur atom of cysteine catalyzed by the DndA and SspA cysteine desulfurases, respectively. Despite playing the same biochemical role, SspA cannot be functionally replaced by DndA, indicating its unique physiological properties. In this study, we solved the crystal structure of Vibrio cyclitrophicus SspA in complex with its natural substrate, cysteine, and cofactor, pyridoxal phosphate (PLP), at a resolution of 1.80 Å. Our solved structure revealed the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor, suggesting a common binding mode shared by cysteine desulfurases. In addition, although the distance between the catalytic Cys314 and the substrate cysteine is 8.9 Å, which is too far for direct interaction, our structural modeling and biochemical analysis revealed a conformational change in the active site region toward the cysteine substrate to move them close to each other to facilitate the nucleophilic attack. Finally, the pulldown analysis showed that SspA could form a complex with SspD, an ATP pyrophosphatase, suggesting that SspD might potentially accept the activated sulfur atom directly from SspA, providing further insights into the biochemical pathway of Ssp-mediated PT modification. IMPORTANCE Apart from its roles in Fe-S cluster assembly, tRNA thiolation, and sulfur-containing cofactor biosynthesis, cysteine desulfurase serves as a sulfur donor in the DNA PT modification, in which a sulfur atom substitutes a nonbridging oxygen in the DNA phosphodiester backbone. The initial sulfur mobilization from l-cysteine is catalyzed by the SspA cysteine desulfurase in the SspABCD-mediated DNA PT modification system. By determining the crystal structure of SspA, the study presents the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor. To overcome the long distance (8.9 Å) between the catalytic Cys314 and the cysteine substrate, a conformational change occurs to bring Cys314 to the vicinity of the substrate, allowing for nucleophilic attack.

scholarly journals Crystal structure of Pistol, a class of self-cleaving ribozyme

2017 ◽  
Vol 114 (5) ◽  
pp. 1021-1026 ◽  
Author(s):  
Laura A. Nguyen ◽  
Jimin Wang ◽  
Thomas A. Steitz
Keyword(s):  
Crystal Structure ◽  
Rna Structure ◽  
Tertiary Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Nonbridging Oxygen ◽  
Close Proximity ◽  
Domains Of Life ◽  
Guanine Base ◽  
A Minor

Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2′-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5′ leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

Nucleophilic Attack on Some Isothiazolium Salts

1973 ◽  
Vol 51 (18) ◽  
pp. 3081-3086 ◽  
Author(s):  
David M. Mckinnon ◽  
Mohamed E. Hassan
Keyword(s):  
Hydrogen Sulfide ◽  
Sulfur Atom ◽  
Nucleophilic Attack ◽  
Isothiazolium Salts

A variety of isothiazolium salts has been prepared and allowed to react with sodium benzoylacetate. 2-Benzoylthiophenes are obtained, suggesting that the position of initial nucleophilic attack is at the sulfur atom of the heterocyclic cation. Reaction with hydrogen sulfide gave acyclic reduction products, or 1,2-dithiole derivatives, depending on the type of substituent on nitrogen in the isothiazolium salts.

scholarly journals Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Howard Gamper ◽  
Haixing Li ◽  
Isao Masuda ◽  
D. Miklos Robkis ◽  
Thomas Christian ◽  
...  
Keyword(s):  
Amino Acids ◽  
Conformational Change ◽  
Molecular Mechanism ◽  
Late Stage ◽  
Anticodon Loop ◽  
Pairing Mechanism ◽  
Extra Nucleotide ◽  
In Cells

AbstractWhile genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 frameshifting involves perturbation of an essential ribosome conformational change that facilitates tRNA-mRNA movements at a late stage of the translocation reaction. Our results provide a molecular mechanism for SufB2-induced +1 frameshifting and suggest that engineering of a specific ribosome conformational change can improve the efficiency of genome recoding.

Crystal Structure, Spectroscopic and Redox Properties of Copper(II) Bis{2-[(2,6-dimethylphenyl)iminomethyl-3-methoxyphenolate]}

2007 ◽  
Vol 62 (9) ◽  
pp. 1133-1138 ◽  
Author(s):  
Veli T. Kasumov ◽  
Ibrahim Uçar ◽  
Ahmet Bulut ◽  
Fevzi Kösal
Keyword(s):  
Crystal Structure ◽  
Title Complex ◽  
Redox Properties ◽  
Orthorhombic Space Group ◽  
Long Distance ◽  
X Ray ◽  
X Ray Crystallography ◽  
Square Planar ◽  
Planar Molecules ◽  
Exchange Interaction Parameter

The coordination chemistry of N-(2,6-di-methylphenyl)-2-hydroxy-3-methoxybenzaldimine (1) with Cu(II) has been investigated by X-ray crystallography, electronic and EPR spectroscopies, as well as by electro- and magnetochemistry. The title complex 2 crystallizes in the orthorhombic space group P212121 (a = 8.1538, b = 17.7466, c =19.8507 Å). The mononuclear square-planar molecules 2 featuring trans-N2O2 coordination are connected via weak intermolecular C-H· · ·π interactions into infinite chains parallel to the a axis. Although the intermolecular Cu· · ·Cu separations within individual chains and between chains are very long (8.154 and 9.726 Å ), the exchange interaction parameter G = 2.03 < 4, estimated from solid state EPR spectra, suggests the existence of long-distance superexchange pathways between adjacent Cu(II) centers. The electronic and electrochemical features of the compound are also discussed.

scholarly journals QUANTUM-CHEMICAL STUDY OF THE REACTION MECHANISM 1,2-ETHANEDIIOL WITH 1,3-DICHLOROPROPENE

2020 ◽  
Vol 2018 (1) ◽  
pp. 56-57
Author(s):  
Elena Chirkina ◽  
Leonid Krivdin ◽  
Nikolay Korchevin
Keyword(s):  
Carbon Atom ◽  
Sulfur Atom ◽  
Density Functional ◽  
Quantum Chemical Study ◽  
Thiol Group ◽  
Chemical Study ◽  
Nucleophilic Attack ◽  
Substitution Product ◽  
Reaction Proceeds ◽  
Theoretical Mechanism

The theoretical mechanism of the interaction of 1,3-dichloropropene with 1,2- ethanedithiol in the system "hydrazine hydrate-KOH" has been proposed by the method of B3LYP / 6- 311 ++ G (d, p) in the framework of the theory of the electron-density functional according to which the reaction proceeds successively in several stages, including the nucleophilic substitution of the chlorine atom present in the sp3-hybridized carbon atom with a sulfur atom to form a mono-substitution product that undergoes a prototropic allylic rearrangement that migrates the double bond to the sulfur atom, followed by closure in the dithiolane cycle due to the nucleophilic attack of the sulfide anion of the second thiol group of the reagent per carbon atom located in the γ-position with respect to the second chlorine atom.

scholarly journals THEORETICAL STUDY OF THE REACTION MECHANISM 1,2-ETHANEDIIOL WITH 1,3-DICHLOROPROPENE

2020 ◽  
Vol 2018 (1) ◽  
pp. 68-77
Author(s):  
Elena Chirkina ◽  
Leonid Krivdin ◽  
Nikolay Korchevin
Keyword(s):  
Carbon Atom ◽  
Chlorine Atom ◽  
Sulfur Atom ◽  
Density Functional ◽  
Theoretical Study ◽  
Thiol Group ◽  
Nucleophilic Attack ◽  
Substitution Product ◽  
Reaction Proceeds ◽  
Theoretical Mechanism

The theoretical mechanism of the interaction of 1,3-dichloropropene with 1,2-ethanedithiol in the system "hydrazine hydrate-KOH" has been proposed by the method of B3LYP / 6-311 ++ G (d, p) in the framework of the theory of the electron-density functional according to which the reaction proceeds successively in several stages, including the nucleophilic substitution of the chlorine atom present in the sp3-hybridized carbon atom with a sulfur atom to form a mono-substitution product that undergoes a prototropic allylic rearrangement that migrates the double bond to the sulfur atom, followed by closure in the dithiolane cycle due to the nucleophilic attack of the sulfide anion of the second thiol group of the reagent per carbon atom located in the γ-position with respect to the second chlorine atom.

scholarly journals Double Lock the COVID 19: Inhibit SARS COV 2 Replication and Suppress Inflammation Cytokine Level by the Golden Compounds

2020 ◽  
Author(s):  
Zhesheng He ◽  
Chunyu Zhang ◽  
Zhongying Du ◽  
Wencong Zhao ◽  
Wenchao Niu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cell Viability ◽  
Sulfur Atom ◽  
Gold Cluster ◽  
Cytokine Level ◽  
Pharmacokinetic Studies ◽  
Down Regulation ◽  
Toxicity Studies ◽  
Tnf Α

Our studies implied the golden compounds may be more effective against COVID 19 as they synergy inhibit SARS COV 2 replication and down regulation inflammation cytokine level. Our crystal structure studies firstly revealed Au (I) ions, derived from auranofin (AF) or gold cluster (GA), covalently bind sulfur atom of Cys145 and Cys156 of Mpro of SARS COV 2. The auranofin or gold cluster well inhibit Mpro activity in vitro. Auranofin or gold cluster could well suppress inflammation cytokine level of IL 6, IL 1β, TNF α via down regulation NF κB activation in macrophage. The cell viability and rat toxicity studies show gold cluster is more safety when compared FDA approved auranofin. The rat pharmacokinetic studies of gold cluster revealed its good bioavailability.

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