scholarly journals Structural and biochemical studies define Nudt12 as a new class of RNA deNADding enzyme in mammalian cells

2018 ◽  
Author(s):  
Ewa Grudzien-Nogalska ◽  
Yixuan Wu ◽  
Xinfu Jiao ◽  
Huijuan Cui ◽  
Ronald P. Hart ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Basis ◽  
Mammalian Cells ◽  
Metabolic Stress ◽  
Cellular Metabolism ◽  
New Class ◽  
Mrna Targets ◽  
Biochemical Studies ◽  
Cellular Energetics ◽  
In Cells

ABSTRACTWe recently demonstrated mammalian cells harbor NAD-capped mRNAs that are hydrolyzed by the DXO deNADding enzyme. Here we report the Nudix protein Nudt12 is a second mammalian deNADding enzyme structurally and mechanistically distinct from DXO and targets different RNAs. Crystal structure of mouse Nudt12 in complex with the deNADding product AMP and three Mg2+ ions at 1.6 Å resolution provides exquisite insights into the molecular basis of the deNADding activity within the NAD pyrophosphate. Disruption of the Nudt12 gene stabilizes transfected NAD-capped RNA in cells and its endogenous NAD-capped mRNA targets are enriched in those encoding proteins involved in cellular energetics. Furthermore, exposure of cells to metabolic stress manifests changes in NAD-capped RNA levels indicating an association between NAD-capped RNAs and cellular metabolism. Lastly, we show that the bacterial RppH protein also possesses deNADding activity toward NAD-capped RNA but not free NAD, revealing a third class of deNADding enzymes.

scholarly journals Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs

2020 ◽  
Vol 48 (12) ◽  
pp. 6788-6798 ◽  
Author(s):  
Sunny Sharma ◽  
Ewa Grudzien-Nogalska ◽  
Keith Hamilton ◽  
Xinfu Jiao ◽  
Jun Yang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Nicotinamide Adenine Dinucleotide ◽  
Mammalian Cells ◽  
Flavin Adenine Dinucleotide ◽  
Nicotinamide Adenine ◽  
Nudix Hydrolase ◽  
Decapping Enzymes ◽  
Hydrolysis Of ◽  
In Cells

Abstract We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5′caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins—Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.

Targeting IDH Mutations in AML: Wielding the Double-edged Sword of Differentiation

2020 ◽  
Vol 20 (7) ◽  
pp. 490-500 ◽  
Author(s):  
Justin S. Becker ◽  
Amir T. Fathi
Keyword(s):  
Genome Structure ◽  
Cellular Metabolism ◽  
Standard Of Care ◽  
Competitive Inhibitor ◽  
Driver Mutations ◽  
New Class ◽  
Regulatory Enzymes ◽  
Idh Mutations ◽  
Genomic Characterization

The genomic characterization of acute myeloid leukemia (AML) by DNA sequencing has illuminated subclasses of the disease, with distinct driver mutations, that might be responsive to targeted therapies. Approximately 15-23% of AML genomes harbor mutations in one of two isoforms of isocitrate dehydrogenase (IDH1 or IDH2). These enzymes are constitutive mediators of basic cellular metabolism, but their mutated forms in cancer synthesize an abnormal metabolite, 2- hydroxyglutarate, that in turn acts as a competitive inhibitor of multiple gene regulatory enzymes. As a result, leukemic IDH mutations cause changes in genome structure and gene activity, culminating in an arrest of normal myeloid differentiation. These discoveries have motivated the development of a new class of selective small molecules with the ability to inhibit the mutant IDH enzymes while sparing normal cellular metabolism. These agents have shown promising anti-leukemic activity in animal models and early clinical trials, and are now entering Phase 3 study. This review will focus on the growing preclinical and clinical data evaluating IDH inhibitors for the treatment of IDH-mutated AML. These data suggest that inducing cellular differentiation is central to the mechanism of clinical efficacy for IDH inhibitors, while also mediating toxicity for patients who experience IDH Differentiation Syndrome. Ongoing trials are studying the efficacy of IDH inhibitors in combination with other AML therapies, both to evaluate potential synergistic combinations as well as to identify the appropriate place for IDH inhibitors within existing standard-of-care regimens.

scholarly journals Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate

2015 ◽  
Vol 71 (2) ◽  
pp. 199-205 ◽  
Author(s):  
George T. Lountos ◽  
Scott Cherry ◽  
Joseph E. Tropea ◽  
David S. Waugh
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Phosphatase Activity ◽  
Small Molecule ◽  
Molecular Basis ◽  
Protein Tyrosine Phosphatases ◽  
Simple Method ◽  
Dual Specificity Phosphatase ◽  
Dual Specificity ◽  
Nitrophenyl Phosphate

4-Nitrophenyl phosphate (p-nitrophenyl phosphate, pNPP) is widely used as a small molecule phosphotyrosine-like substrate in activity assays for protein tyrosine phosphatases. It is a colorless substrate that upon hydrolysis is converted to a yellow 4-nitrophenolate ion that can be monitored by absorbance at 405 nm. Therefore, the pNPP assay has been widely adopted as a quick and simple method to assess phosphatase activity and is also commonly used in assays to screen for inhibitors. Here, the first crystal structure is presented of a dual-specificity phosphatase, human dual-specificity phosphatase 22 (DUSP22), in complex with pNPP. The structure illuminates the molecular basis for substrate binding and may also facilitate the structure-assisted development of DUSP22 inhibitors.

The Crystal Structure of the C-Terminal DAP5/p97 Domain Sheds Light on the Molecular Basis for Its Processing by Caspase Cleavage

2008 ◽  
Vol 383 (3) ◽  
pp. 539-548 ◽  
Author(s):  
Noa Liberman ◽  
Orly Dym ◽  
Tamar Unger ◽  
Shira Albeck ◽  
Yoav Peleg ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Basis ◽  
Caspase Cleavage

A New Class of Oxide Superconductor (Nd, Ce, Sr)2CuO4

1989 ◽  
Vol 156 ◽  
Author(s):  
E. Takayama-Muromachi
Keyword(s):  
Crystal Structure ◽  
Crystal Chemistry ◽  
Superconducting Phase ◽  
Type Structure ◽  
Oxide Superconductor ◽  
New Class ◽  
System 2 ◽  
New Type ◽  
System 1 ◽  
Tetragonal Cell

ABSTRACTSince the discovery of the high-Tc superconductor in the La-Ba-Cu-O system [1], a great deal of experimental and theoretical effort have been made to clarify the nature of the Cu-based oxides. In order to elucidate mechanism of the high-Tc superconductivity, discovery of a new type of superconductor is no doubt of great importance. Recently, Akimitsu et al. found a new oxide superconductor in the Nd-Ce-Sr-Cu-O system [2]. Soon after their discovery, the superconducting phase was isolated and identified [3]. It has a tetragonal cell with space group P4/nmm and has a structure closely related to but different from the K2NiF4− or T'-Nd2CuO4− -type structure. Although, Tc of the Nd-Ce-Sr-Cu oxide is not so high (ca. 20 K) compared with the 1–2–3 or Bi(Tl)-based superconductors, it has aroused interest widely due to a very simple crystal structure. In this article, I will discuss superconductivity and crystal chemistry of the Nd-Ce-Sr-Cu oxide. Also, various compounds isostructural to it will be presented.

Glutamate-like immunoreactivity in the cat superior colliculus and visual cortex: Further evidence that glutamate is the neurotransmitter of the corticocollicular pathway

1997 ◽  
Vol 14 (1) ◽  
pp. 27-37 ◽  
Author(s):  
Chang-Jin Jeon ◽  
Michael K. Hartman ◽  
R. Ranney Mize
Keyword(s):  
Visual Cortex ◽  
Superior Colliculus ◽  
Optical Density ◽  
Retrograde Tracing ◽  
Biochemical Studies ◽  
Deep Layers ◽  
Dense Band ◽  
Cat Superior Colliculus ◽  
Made In ◽  
In Cells

AbstractBiochemical studies provide evidence that the pathway from visual cortex to the superior colliculus (SC) utilizes glutamate as a neurotransmitter. In the present study, we have used immunocytochemistry, visual cortex lesions, and retrograde tracing to show directly by anatomical methods that glutamate or a closely related analog is contained in corticocollicular neurons and terminals. A monoclonal antibody directed against gamma-L-glutamyl-L-glutamate (gamma glu glu) was used to localize glutamate-like immunoreactivity in both the superior colliculus (SC) and visual cortex (VC). Unilateral lesions of areas 17–18 were made in four cats to determine if gamma glu glu labeling was reduced in SC by this lesion. WGA-HRP was injected into the SC of 10 additional cats in order to determine if corticocollicular neurons were also labeled by the gamma glu glu antibody. A distinctive dense band of gamma glu glu immunoreactivity was found within the deep superficial gray and upper optic layers of SC where many corticotectal axons are known to terminate. Both fibers and cells were labeled within the band. Immunoreactivity was also found in cells and fibers throughout the deep layers of SC. Measures of total immunoreactivity (i.e. optical density) in the dense band were made in sections from the SC both ipsilateral to and contralateral to the lesions of areas 17–18. A consistent reduction in optical density was found in both the neuropil and in cells within the dense band of the SC ipsilateral to the lesion. A large percentage of all corticocollicular neurons that were retrogradely labeled by WGA-HRP also contained gamma glu glu. These results provide further evidence that the corticocollicular pathway in mammals is glutamatergic. The results also suggest that visual cortex ablation alters synthesis or storage of glutamate within postsynaptic SC neurons, presumably as a result of partial deafferentation.

Sign in / Sign up

Export Citation Format

Share Document