scholarly journals Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gloria Gamiz-Arco ◽  
Luis I. Gutierrez-Rus ◽  
Valeria A. Risso ◽  
Beatriz Ibarra-Molero ◽  
Yosuke Hoshino ◽  
...  
Keyword(s):  
Sequence Space ◽  
Conformational Flexibility ◽  
Allosteric Modulation ◽  
Heme Binding ◽  
Optimum Temperature ◽  
Glycosidic Bonds ◽  
Glycosidase Activity ◽  
Tim Barrel ◽  
Crystallographic Structures ◽  
Ancestral Protein

AbstractGlycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.

scholarly journals Novel heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

2020 ◽  
Author(s):  
Gloria Gamiz-Arco ◽  
Luis I. Gutierrez-Rus ◽  
Valeria A. Risso ◽  
Beatriz Ibarra-Molero ◽  
Yosuke Hoshino ◽  
...  
Keyword(s):  
Sequence Space ◽  
Conformational Flexibility ◽  
Allosteric Modulation ◽  
Heme Binding ◽  
Optimum Temperature ◽  
Glycosidic Bonds ◽  
Glycosidase Activity ◽  
Tim Barrel ◽  
Crystallographic Structures ◽  
Ancestral Protein

ABSTRACTGlycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ~5500 reported crystallographic structures of ~1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.

scholarly journals Resurrected Ancestral TIM-Barrel Glycosidase Displays Heme Binding and Allosteric Modulation

2021 ◽  
Vol 120 (3) ◽  
pp. 125a-126a
Author(s):  
Luis I. Gutierrez-Rus ◽  
Gloria Gamiz-Arco ◽  
Valeria A. Risso ◽  
Beatriz Ibarra-Molero ◽  
Yosuke Hoshino ◽  
...  
Keyword(s):  
Allosteric Modulation ◽  
Heme Binding ◽  
Tim Barrel

scholarly journals Allosteric modulation of anti-HIV drug and ferric heme binding to human serum albumin

FEBS Journal ◽  
2005 ◽  
Vol 272 (24) ◽  
pp. 6287-6296 ◽  
Author(s):  
Alessio Bocedi ◽  
Stefania Notari ◽  
Enea Menegatti ◽  
Gabriella Fanali ◽  
Mauro Fasano ◽  
...  
Keyword(s):  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Allosteric Modulation ◽  
Heme Binding ◽  
Ferric Heme ◽  
Anti Hiv

scholarly journals Amylolytic enzymes - focus on the alpha-amylases from Archae and plants

2021 ◽  
Vol 9 (1) ◽  
pp. 5-26
Author(s):  
Štefan Janeček
Keyword(s):  
Three Dimensional ◽  
Structural Features ◽  
Catalytic Triad ◽  
Amino Acid Sequences ◽  
Glycoside Hydrolases ◽  
Amylolytic Enzymes ◽  
Conserved Sequence ◽  
Glycosidic Bonds ◽  
Evolutionary Relatedness ◽  
Tim Barrel

Amylolytic enzymes represent a group of starch hydrolases and related enzymes that are active towards the α-glycosidic bonds in starch and related poly- and oligosaccharides. The three best known amylolytic enzymes are α-amylase, β-amylase and glucoamylase that, however, differ from each other by their amino acid sequences, three-dimensional structures, reaction mechanisms and catalytic machineries. In the sequence-based classification of all glycoside hydrolases (GHs) they have therefore been classified into the three independent families: GH13 (α-amylases), GH14 (β-amylases) and GH15 (glucoamylases). Some amylolytic enzymes have been placed to the families GH31 and GH57. The family GH13 together with the families GH70 and GH77 constitutes the clan GH-H, well-known as the α-amylase family. It contains more than 6,000 sequences and covers 30 various enzyme specificities sharing the conserved sequence regions, catalytic TIM-barrel fold, retaining reaction mechanism and catalytic triad. Among the GH13 α-amylases, those produced by plants and archaebacteria exhibit common sequence similarities that distinguish them from the α-amylases of the remaining taxonomic sources. Despite the close evolutionary relatedness between the plant and archaeal α-amylases, there are also specific differences that discriminate them from each other. These specific differences could be used in an effort to reveal the sequence-structural features responsible for the high thermostability of the α-amylases from Archaea.

Unprecedented conformational flexibility revealed in the ligand-binding domains of theBovicola ovisecdysone receptor (EcR) and ultraspiracle (USP) subunits

2014 ◽  
Vol 70 (7) ◽  
pp. 1954-1964 ◽  
Author(s):  
Bin Ren ◽  
Thomas S. Peat ◽  
Victor A. Streltsov ◽  
Matthew Pollard ◽  
Ross Fernley ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Pocket ◽  
Conformational Flexibility ◽  
Order Structure ◽  
Ecdysone Receptor ◽  
Binding Region ◽  
X Ray ◽  
Receptor Structure ◽  
Binding Domains ◽  
Crystallographic Structures

The heterodimeric ligand-binding region of theBovicola ovisecdysone receptor has been crystallized either in the presence of an ecdysteroid or a synthetic methylene lactam insecticide. Two X-ray crystallographic structures, determined at 2.7 Å resolution, show that the ligand-binding domains of both subunits of this receptor, like those of other nuclear receptors, can display significant conformational flexibility. Thermal melt experiments show that while ponasterone A stabilizes the higher order structure of the heterodimer in solution, the methylene lactam destabilizes it. The conformations of the EcR and USP subunits observed in the structure crystallized in the presence of the methylene lactam have not been seen previously in any ecdysone receptor structure and represent a new level of conformational flexibility for these important receptors. Interestingly, the new USP conformation presents an open, unoccupied ligand-binding pocket.

Allosteric modulation of myristate and Mn(III)heme binding to human serum albumin. Optical and NMR spectroscopy characterization

FEBS Journal ◽  
2005 ◽  
Vol 272 (18) ◽  
pp. 4672-4683 ◽  
Author(s):  
Gabriella Fanali ◽  
Riccardo Fesce ◽  
Cristina Agrati ◽  
Paolo Ascenzi ◽  
Mauro Fasano
Keyword(s):  
Nmr Spectroscopy ◽  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Allosteric Modulation ◽  
Heme Binding

Structure of a new orthorhombic phase in NiTi: Mn shape memory alloys

1990 ◽  
Vol 48 (4) ◽  
pp. 1000-1001
Author(s):  
Jenö Beyer ◽  
Lajos Tóth
Keyword(s):  
Martensitic Transformation ◽  
Structural Changes ◽  
High Vacuum ◽  
Intermetallic Phase ◽  
Orthorhombic Phase ◽  
Transformation Process ◽  
Analytical Electron ◽  
Analytical Electron Microscope ◽  
Crystallographic Structures ◽  
Ternary Additions

The structural changes during reversible martensitic transformation of near-equiatomic NiTi alloys can best be studied in TEM at around room temperature. Ternary additions like Mn offer this possibility by suppressing the Ms temperature below RT. Besides the stable intermetallic phases (Ti2Ni, TiNi, TiNi3) several metastable phases with various crystallographic structures (rhombohedral, hexagonal, monoclinic, cubic) have also been reported to precipitate due to suitable annealing procedures.TiNi:Mn samples with 0.9 and 1.3 at% Mn were arc melted in argon atmosphere and homogenized at 948 °C for 72 hours in high vacuum in an infrared furnace. After spark cutting slices of 0.2 mm, TEM specimens were prepared by electrochemical polishing with the twin-jet technique in methanol - perchloric acid electrolyte. The TEM study was carried out in a JEOL 200 CX analytical electron microscope.In this paper a new intermetallic phase is reported which has been observed in both samples by TEM during the martensitic transformation process.

The Structural Landscape of SARS-CoV-2 Main Protease: Hints for Inhibitor Search.

2020 ◽  
Author(s):  
Luigi Leonardo Palese
Keyword(s):  
Comparative Analysis ◽  
Global Health ◽  
Binding Site ◽  
Causative Agent ◽  
Data Set ◽  
Substrate Binding Site ◽  
Global Pandemic ◽  
Main Protease ◽  
Crystallographic Structures ◽  
Structural Aspects

In 2019, an outbreak occurred which resulted in a global pandemic. The causative agent of this serious global health threat was a coronavirus similar to the agent of SARS, referred to as SARS-CoV-2. In this work an analysis of the available structures of the SARS-CoV-2 main protease has been performed. From a data set of crystallographic structures the dynamics of the protease has been obtained. Furthermore, a comparative analysis of the structures of SARS-CoV-2 with those of the main protease of the coronavirus responsible of SARS (SARS-CoV) was carried out. The results of these studies suggest that, although main proteases of SARS-CoV and SARS-CoV-2 are similar at the backbone level, some plasticity at the substrate binding site can be observed. The consequences of these structural aspects on the search for effective inhibitors of these enzymes are discussed, with a focus on already known compounds. The results obtained show that compounds containing an oxirane ring could be considered as inhibitors of the main protease of SARS-CoV-2.

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