scholarly journals Structural and functional insights into Archaeoglobus fulgidus m2G10 tRNA methyltransferase Trm11 and its Trm112 activator

2020 ◽  
Vol 48 (19) ◽  
pp. 11068-11082
Author(s):  
Can Wang ◽  
Nhan van Tran ◽  
Vincent Jactel ◽  
Vincent Guérineau ◽  
Marc Graille
Keyword(s):  
Enzymatic Activity ◽  
Crystal Structures ◽  
Neurodevelopmental Disorders ◽  
Mrna Translation ◽  
Archaeoglobus Fulgidus ◽  
Translation Process ◽  
Modifying Factors ◽  
Single Protein ◽  
Trna Methyltransferase ◽  
Allosteric Activator

Abstract tRNAs play a central role during the translation process and are heavily post-transcriptionally modified to ensure optimal and faithful mRNA decoding. These epitranscriptomics marks are added by largely conserved proteins and defects in the function of some of these enzymes are responsible for neurodevelopmental disorders and cancers. Here, we focus on the Trm11 enzyme, which forms N2-methylguanosine (m2G) at position 10 of several tRNAs in both archaea and eukaryotes. While eukaryotic Trm11 enzyme is only active as a complex with Trm112, an allosteric activator of methyltransferases modifying factors (RNAs and proteins) involved in mRNA translation, former studies have shown that some archaeal Trm11 proteins are active on their own. As these studies were performed on Trm11 enzymes originating from archaeal organisms lacking TRM112 gene, we have characterized Trm11 (AfTrm11) from the Archaeoglobus fulgidus archaeon, which genome encodes for a Trm112 protein (AfTrm112). We show that AfTrm11 interacts directly with AfTrm112 similarly to eukaryotic enzymes and that although AfTrm11 is active as a single protein, its enzymatic activity is strongly enhanced by AfTrm112. We finally describe the first crystal structures of the AfTrm11-Trm112 complex and of Trm11, alone or bound to the methyltransferase inhibitor sinefungin.

scholarly journals Negative allosteric regulation of Enterococcus faecalis small alarmone synthetase RelQ by single-stranded RNA

2017 ◽  
Vol 114 (14) ◽  
pp. 3726-3731 ◽  
Author(s):  
Jelena Beljantseva ◽  
Pavel Kudrin ◽  
Liis Andresen ◽  
Victoria Shingler ◽  
Gemma C. Atkinson ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Enterococcus Faecalis ◽  
Rna Binding ◽  
Regulatory Mechanism ◽  
Allosteric Regulation ◽  
Rna Binding Protein ◽  
Growth Stress ◽  
Stress Adaptation ◽  
Single Protein ◽  
Allosteric Activator

The alarmone nucleotides guanosine pentaphosphate (pppGpp) and tetraphosphate (ppGpp), collectively referred to as (p)ppGpp, are key regulators of bacterial growth, stress adaptation, pathogenicity, and antibiotic tolerance. We show that the tetrameric small alarmone synthetase (SAS) RelQ from the Gram-positive pathogen Enterococcus faecalis is a sequence-specific RNA-binding protein. RelQ’s enzymatic and RNA binding activities are subject to intricate allosteric regulation. (p)ppGpp synthesis is potently inhibited by the binding of single-stranded RNA. Conversely, RelQ’s enzymatic activity destabilizes the RelQ:RNA complex. pppGpp, an allosteric activator of the enzyme, counteracts the effect of RNA. Tetramerization of RelQ is essential for this regulatory mechanism, because both RNA binding and enzymatic activity are abolished by deletion of the SAS-specific C-terminal helix 5α. The interplay of pppGpp binding, (p)ppGpp synthesis, and RNA binding unites two archetypal regulatory paradigms within a single protein. The mechanism is likely a prevalent but previously unappreciated regulatory switch used by the widely distributed bacterial SAS enzymes.

scholarly journals Autophosphorylation of Archaeoglobus fulgidus Rio2 and crystal structures of its nucleotide-metal ion complexes

FEBS Journal ◽  
2005 ◽  
Vol 272 (11) ◽  
pp. 2800-2810 ◽  
Author(s):  
Nicole LaRonde-LeBlanc ◽  
Tad Guszczynski ◽  
Terry Copeland ◽  
Alexander Wlodawer
Keyword(s):  
Crystal Structures ◽  
Metal Ion ◽  
Archaeoglobus Fulgidus ◽  
Metal Ion Complexes

Natural inhibitors of thrombin

2014 ◽  
Vol 111 (04) ◽  
pp. 583-589 ◽  
Author(s):  
James Huntington
Keyword(s):  
Blood Flow ◽  
Crystal Structures ◽  
Active Site ◽  
Anion Binding ◽  
Thrombin Inhibitors ◽  
Multiple Functions ◽  
Endogenous Inhibitors ◽  
Active Site Cleft ◽  
Single Protein ◽  
Natural Inhibitors

SummaryThe serine protease thrombin is the effector enzyme of blood coagulation. It has many activities critical for the formation of stable clots, including cleavage of fibrinogen to fibrin, activation of platelets and conversion of procofactors to active cofactors. Thrombin carries-out its multiple functions by utilising three special features: a deep active site cleft and two anion binding exosites (exosite I and II). Similarly, thrombin inhibitors have evolved to exploit the unique features of thrombin to achieve rapid and specific inactivation of thrombin. Exogenous thrombin inhibitors come from several different protein families and are generally found in the saliva of haematophagous animals (blood suckers) as part of an anticoagulant cocktail that allows them to feed. Crystal structures of several of these inhibitors reveal how peptides and proteins can be targeted to thrombin in different and interesting ways. Thrombin activity must also be regulated by endogenous inhibitors so that thrombi do not occlude blood flow and cause thrombosis. A single protein family, the serpins, provides all four of the endogenous thrombin inhibitors found in man. The crystal structures of these serpins bound to thrombin have been solved, revealing a similar exosite-dependence on complex formation. In addition to forming the recognition complex, serpins destroy the structure of thrombin, allowing them to be released from cofactors and substrates for clearance. This review examines how the special features of thrombin have been exploited by evolution to achieve inhibition of the ultimate coagulation protease.

scholarly journals AG-348 (Mitapivat), an allosteric activator of red blood cell pyruvate kinase, increases enzymatic activity, protein stability, and ATP levels over a broad range of PKLR genotypes

Haematologica ◽  
2020 ◽  
Vol 106 (1) ◽  
pp. 238-249 ◽  
Author(s):  
Minke A.E. Rab ◽  
Brigitte A. Van Oirschot ◽  
Penelope A. Kosinski ◽  
Jeffrey Hixon ◽  
Kendall Johnson ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Enzymatic Activity ◽  
Pyruvate Kinase ◽  
Ex Vivo ◽  
Residual Activity ◽  
Red Cell ◽  
Atp Levels ◽  
Erythroid Precursors ◽  
Premature Removal ◽  
Allosteric Activator

Pyruvate kinase (PK) deficiency is a rare hereditary disorder affecting red cell (RBC) glycolysis, causing changes in metabolism including a deficiency in ATP. This affects red cell homeostasis, promoting premature removal of RBCs from the circulation. In this study we characterized and evaluated the effect of AG-348, an allosteric activator of PK that is currently in clinical trials for treatment of PK deficiency, on RBCs and erythroid precursors from PK-deficient patients. In 15 patients ex vivo treatment with AG-348 resulted in increased enzymatic activity in all patient cells after 24 hours (mean increase 1.8-fold, range 1.2-3.4). ATP levels increased (mean increase 1.5-fold, range 1.0-2.2) similar to control cells (mean increase 1.6-fold, range, 1.4-1.8). Generally, PK thermostability was strongly reduced in PK-deficient RBCs. Ex vivo treatment with AG-348 increased residual activity 1.4 to >10-fold than residual activity of vehicle-treated samples. Protein analyses suggests that a sufficient level of PK protein is required for cells to respond to AG-348 treatment ex-vivo, as treatment effects were minimal in patient cells with very low or undetectable levels of PK-R. In half of the patients, ex vivo treatment with AG-348 was associated with an increase in RBC deformability. These data support the hypothesis that drug intervention with AG-348 effectively upregulates PK enzymatic activity and increases stability in PK-deficient RBCs over a broad range of PKLR genotypes. The concomitant increase in ATP levels suggests that glycolytic pathway activity may be restored. AG-348 treatment may represent an attractive way to correct the underlying pathologies of PK deficiency. (AG-348 is currently in clinical trials for the treatment of PK deficiency. ClinicalTrials.gov: NCT02476916, NCT03853798, NCT03548220, NCT03559699).

scholarly journals Crystal Structures of a Tetrahedral Open Pore Ferritin from the Hyperthermophilic Archaeon Archaeoglobus fulgidus

Structure ◽  
2005 ◽  
Vol 13 (4) ◽  
pp. 637-648 ◽  
Author(s):  
Eric Johnson ◽  
Duilio Cascio ◽  
Michael R. Sawaya ◽  
Mari Gingery ◽  
Imke Schröder
Keyword(s):  
Crystal Structures ◽  
Archaeoglobus Fulgidus ◽  
Hyperthermophilic Archaeon

scholarly journals Unveiling sequential late-stage methyltransferase reactions in the meleagrin/oxaline biosynthetic pathway

2018 ◽  
Vol 16 (35) ◽  
pp. 6450-6459 ◽  
Author(s):  
Sean A. Newmister ◽  
Stelamar Romminger ◽  
Jennifer J. Schmidt ◽  
Robert M. Williams ◽  
Janet L. Smith ◽  
...  
Keyword(s):  
Natural Products ◽  
Enzymatic Activity ◽  
Crystal Structures ◽  
Late Stage ◽  
Biosynthetic Pathway ◽  
Fungal Natural Products

Enzymatic activity and crystal structures of the methyltransferases involved in the biosynthesis of fungal natural products meleagrin and oxaline.

scholarly journals Crystal structures of a yeast 14-3-3 protein fromLachancea thermotoleransin the unliganded form and bound to a human lipid kinase PI4KB-derived peptide reveal high evolutionary conservation

2016 ◽  
Vol 72 (11) ◽  
pp. 799-803 ◽  
Author(s):  
Andrea Eisenreichova ◽  
Martin Klima ◽  
Evzen Boura
Keyword(s):  
Structural Analysis ◽  
Subcellular Localization ◽  
Enzymatic Activity ◽  
Crystal Structures ◽  
Evolutionary Conservation ◽  
Ligand Recognition ◽  
Lipid Kinase ◽  
Binding Partners ◽  
Phosphatidylinositol 4 ◽  
Lachancea Thermotolerans

14-3-3 proteins bind phosphorylated binding partners to regulate several of their properties, including enzymatic activity, stability and subcellular localization. Here, two crystal structures are presented: the crystal structures of the 14-3-3 protein (also known as Bmh1) from the yeastLachancea thermotoleransin the unliganded form and bound to a phosphopeptide derived from human PI4KB (phosphatidylinositol 4-kinase B). The structures demonstrate the high evolutionary conservation of ligand recognition by 14-3-3 proteins. The structural analysis suggests that ligand recognition by 14-3-3 proteins evolved very early in the evolution of eukaryotes and remained conserved, underlying the importance of 14-3-3 proteins in physiology.

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