scholarly journals Insights into substrate binding and catalysis in bacterial type I dehydroquinase

2014 ◽  
Vol 462 (3) ◽  
pp. 415-424 ◽  
Author(s):  
María Maneiro ◽  
Antonio Peón ◽  
Emilio Lence ◽  
José M. Otero ◽  
Mark J. Van Raaij ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Binding ◽  
Detailed Knowledge ◽  
Type I ◽  
Conserved Residues ◽  
Binding Process ◽  
Bacterial Type

The crystal structure of S. typhi type I dehydroquinase in complex with (2R)-3-methyl-3-dehydroquinic acid is described. A previously unknown key role of several conserved residues and a detailed knowledge of the substrate binding process is detailed.

scholarly journals Linking the YTH domain to cancer: the importance of YTH family proteins in epigenetics

2021 ◽  
Vol 12 (4) ◽  
Author(s):  
Rongkai Shi ◽  
Shilong Ying ◽  
Yadan Li ◽  
Liyuan Zhu ◽  
Xian Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Epigenetic Regulation ◽  
Mammalian Cells ◽  
Structural Features ◽  
Metabolic Fate ◽  
Conserved Residues ◽  
Cancer Types ◽  
Reversible Modification ◽  
Yth Domain

AbstractN6-methyladenosine (m6A), the most prevalent and reversible modification of mRNA in mammalian cells, has recently been extensively studied in epigenetic regulation. YTH family proteins, whose YTH domain can recognize and bind m6A-containing RNA, are the main “readers” of m6A modification. YTH family proteins perform different functions to determine the metabolic fate of m6A-modified RNA. The crystal structure of the YTH domain has been completely resolved, highlighting the important roles of several conserved residues of the YTH domain in the specific recognition of m6A-modified RNAs. Upstream and downstream targets have been successively revealed in different cancer types and the role of YTH family proteins has been emphasized in m6A research. This review describes the regulation of RNAs by YTH family proteins, the structural features of the YTH domain, and the connections of YTH family proteins with human cancers.

Structural Insight into the Interaction of Sendai Virus C Protein with Alix To Stimulate Viral Budding

2021 ◽  
Author(s):  
Kosuke Oda ◽  
Yasuyuki Matoba ◽  
Masanori Sugiyama ◽  
Takemasa Sakaguchi
Keyword(s):  
Crystal Structure ◽  
Binding Affinity ◽  
Sendai Virus ◽  
Antiviral Drugs ◽  
Accessory Protein ◽  
Type I ◽  
C Protein ◽  
Viral Budding ◽  
C Proteins

The Sendai virus (SeV), belonging to the Respirovirus genus of the family Paramyxoviridae , harbors an accessory protein, named C protein, which facilitates the viral pathogenicity in mice. In addition, the C protein is known to stimulate the budding of virus-like particles through the binding to the host ALG-2 interacting protein X (Alix), a component of the endosomal sorting complexes required for transport (ESCRT) machinery. However, siRNA-mediated gene knockdown studies suggested that neither Alix nor C protein are related to the SeV budding. In the present study, we determined the crystal structure of a complex comprising of the C -terminal half of the C protein (Y3) and the Bro1 domain of Alix at a resolution of 2.2 Å, to investigate the role of the association in the SeV budding. The structure revealed that a novel consensus sequence, LxxW, which is conserved among the Respirovirus C proteins, is important for the Alix-binding. SeV possessing a mutated C protein with a reduced Alix-binding affinity showed impaired virus production, which correlated with the binding affinity. Infectivity analysis showed a 160-fold reduction at 12 h post-infection compared with non-mutated virus, while C protein competes with CHMP4, one subunit of the ESCRT-III complex, on the binding to Alix. Altogether, these results highlight the critical role of C protein in the SeV budding. IMPORTANCE Human parainfluenza virus type I (hPIV1) is a respiratory pathogen affecting in young children, immunocompromised patients, and the elderly, with no available vaccines or antiviral drugs. Sendai virus (SeV), a murine counterpart of hPIV1, has been extensively studied to determine the molecular and biological properties of hPIV1. These viruses possess a multifunctional accessory protein, C protein, which is essential for stimulating the viral reproduction, however, its role in budding remains controversial. In the present study, the crystal structure of the C -terminal half of the SeV C protein associated with the Bro1 domain of Alix, a component of a cell membrane modulating machinery ESCRT, was elucidated. Based on the structure, we designed mutated C proteins with different binding affinity to Alix, and showed that the interaction between C and Alix is vital for the viral budding. These findings provide new insights into the development of a new antiviral drugs against hPIV1.

Chromosomal bacterial type II toxin–antitoxin systems

2012 ◽  
Vol 58 (5) ◽  
pp. 553-562 ◽  
Author(s):  
Mohammad Adnan Syed ◽  
Céline M. Lévesque
Keyword(s):  
De Novo ◽  
Physiological Role ◽  
Type I ◽  
Type Ii ◽  
Translation Process ◽  
Bacterial Physiology ◽  
The Subject ◽  
Almost All ◽  
Bacterial Type

Most prokaryotic chromosomes contain a number of toxin–antitoxin (TA) modules consisting of a pair of genes that encode 2 components, a stable toxin and its cognate labile antitoxin. TA systems are also known as addiction modules, since the cells become “addicted” to the short-lived antitoxin product (the unstable antitoxin is degraded faster than the more stable toxin) because its de novo synthesis is essential for their survival. While toxins are always proteins, antitoxins are either RNAs (type I, type III) or proteins (type II). Type II TA systems are widely distributed throughout the chromosomes of almost all free-living bacteria and archaea. The vast majority of type II toxins are mRNA-specific endonucleases arresting cell growth through the mechanism of RNA cleavage, thus preventing the translation process. The physiological role of chromosomal type II TA systems still remains the subject of debate. This review describes the currently known type II toxins and their characteristics. The different hypotheses that have been proposed to explain their role in bacterial physiology are also discussed.

Type I Procollagen C-Propeptide Defects: Study of Genotype-Phenotype Correlation and Predictive Role of Crystal Structure

2014 ◽  
pp. n/a-n/a ◽  
Author(s):  
Sofie Symoens ◽  
David J.S. Hulmes ◽  
Jean-Marie Bourhis ◽  
Paul J. Coucke ◽  
Anne De Paepe ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Type I ◽  
Phenotype Correlation ◽  
Type I Procollagen ◽  
Genotype Phenotype Correlation ◽  
Predictive Role

scholarly journals Clarification of the role of key active site residues of glutathione transferase Zeta/maleylacetoacetate isomerase by a new spectrophotometric technique

2003 ◽  
Vol 374 (3) ◽  
pp. 731-737 ◽  
Author(s):  
Philip G. BOARD ◽  
Matthew C. TAYLOR ◽  
Marjorie COGGAN ◽  
Michael W. PARKER ◽  
Hoffman B. LANTUM ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Glutathione Transferase ◽  
Salt Bridge ◽  
Side Chain ◽  
Active Site Residues ◽  
Conserved Residues ◽  
Isomerase Activity ◽  
Catalytic Role

hGSTZ1-1 (human glutathione transferase Zeta 1-1) catalyses a range of glutathione-dependent reactions and plays an important role in the metabolism of tyrosine via its maleylacetoacetate isomerase activity. The crystal structure and sequence alignment of hGSTZ1 with other GSTs (glutathione transferases) focused attention on three highly conserved residues (Ser-14, Ser-15, Cys-16) as candidates for an important role in catalysis. Progress in the investigation of these residues has been limited by the absence of a convenient assay for kinetic analysis. In this study we have developed a new spectrophotometric assay with a novel substrate [(±)-2-bromo-3-(4-nitrophenyl)propionic acid]. The assay has been used to rapidly assess the potential catalytic role of several residues in the active site. Despite its less favourable orientation in the crystal structure, Ser-14 was the only residue found to be essential for catalysis. It is proposed that a conformational change may favourably reposition the hydroxyl of Ser-14 during the catalytic cycle. The Cys16→Ala (Cys-16 mutated to Ala) mutation caused a dramatic increase in the Km for glutathione, indicating that Cys-16 plays an important role in the binding and orientation of glutathione in the active site. Previous structural studies implicated Arg-175 in the orientation of α-halo acid substrates in the active site of hGSTZ1-1. Mutation of Arg-175 to Lys or Ala resulted in a significant lowering of the kcat in the Ala-175 variant. This result is consistent with the proposal that the charged side chain of Arg-175 forms a salt bridge with the carboxylate of the α-halo acid substrates.

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