scholarly journals Comparison of Spatial Structures and Packaging of Phosphorybosil Pyrophosphate Synthetase 2 from Thermus thermophilus HB27 in Rhombohedral and Tetragonal Crystals

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1128
Author(s):  
Yulia Abramchik ◽  
Evgeniy Zayats ◽  
Maria Kostromina ◽  
Dmitry Lykoshin ◽  
Ilya Fateev ◽  
...  
Keyword(s):  
Thermus Thermophilus ◽  
Thermophilic Bacterium ◽  
Structural Basis ◽  
Lithium Sulfate ◽  
Spatial Structures ◽  
Phosphoribosyl Pyrophosphate ◽  
Space Group ◽  
Tetragonal Crystals ◽  
Protein Molecules ◽  
Enzyme Molecules

We report the spatial structure of phosphoribosyl pyrophosphate synthetase 2 from the thermophilic bacterium Thermus thermophilus HB27 (TthPRPPS2) obtained at a 1.85 Å resolution using a diffraction set collected from rhombohedral crystals (space group R32-h), grown with lithium sulfate as a precipitant. This crystal structure was compared with the structure of TthPRPPS2, previously obtained at a 2.2 Å resolution using diffraction sets from the tetragonal crystals (space group P41212), grown with ammonium sulfate as a precipitant. The comparison of these structures allows the study of the differences between protein molecules in both crystalline structures, as well as the packaging of enzyme molecules in crystals of both spatial groups. Our results may contribute to the research of the structural basis of catalytic activity and substrate specificity of this enzyme.

scholarly journals Characterization of DNA transport in the thermophilic bacterium Thermus thermophilus HB27

FEBS Journal ◽  
2006 ◽  
Vol 273 (18) ◽  
pp. 4210-4218 ◽  
Author(s):  
Cornelia Schwarzenlander ◽  
Beate Averhoff
Keyword(s):  
Thermus Thermophilus ◽  
Thermophilic Bacterium ◽  
Dna Transport

scholarly journals Glutamate Dehydrogenase from Thermus thermophilus Is Activated by AMP and Leucine as a Complex with Catalytically Inactive Adenine Phosphoribosyltransferase Homolog

2019 ◽  
Vol 201 (14) ◽  
Author(s):  
Takeo Tomita ◽  
Hajime Matsushita ◽  
Ayako Yoshida ◽  
Saori Kosono ◽  
Minoru Yoshida ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Glutamate Dehydrogenase ◽  
Ternary Complex ◽  
Thermus Thermophilus ◽  
Thermophilic Bacterium ◽  
Regulatory Subunit ◽  
Binary Complex ◽  
Bacterial Cells ◽  
Adenine Phosphoribosyltransferase ◽  
Content Type

ABSTRACT Glutamate dehydrogenase (GDH) from a thermophilic bacterium, Thermus thermophilus, is composed of two heterologous subunits, GdhA and GdhB. In the heterocomplex, GdhB acts as the catalytic subunit, whereas GdhA lacks enzymatic activity and acts as the regulatory subunit for activation by leucine. In the present study, we performed a pulldown assay using recombinant T. thermophilus, producing GdhA fused with a His tag at the N terminus, and found that TTC1249 (APRTh), which is annotated as adenine phosphoribosyltransferase but lacks the enzymatic activity, was copurified with GdhA. When GdhA, GdhB, and APRTh were coproduced in Escherichia coli cells, they were purified as a ternary complex. The ternary complex exhibited GDH activity that was activated by leucine, as observed for the GdhA-GdhB binary complex. Furthermore, AMP activated GDH activity of the ternary complex, whereas such activation was not observed for the GdhA-GdhB binary complex. This suggests that APRTh mediates the allosteric activation of GDH by AMP. The present study demonstrates the presence of complicated regulatory mechanisms of GDH mediated by multiple compounds to control the carbon-nitrogen balance in bacterial cells. IMPORTANCE GDH, which catalyzes the synthesis and degradation of glutamate using NAD(P)(H), is a widely distributed enzyme among all domains of life. Mammalian GDH is regulated allosterically by multiple metabolites, in which the antenna helix plays a key role to transmit the allosteric signals. In contrast, bacterial GDH was believed not to be regulated allosterically because it lacks the antenna helix. We previously reported that GDH from Thermus thermophilus (TtGDH), which is composed of two heterologous subunits, is activated by leucine. In the present study, we found that AMP activates TtGDH using a catalytically inactive APRTh as the sensory subunit. This suggests that T. thermophilus possesses a complicated regulatory mechanism of GDH to control carbon and nitrogen metabolism.

scholarly journals Expression, purification, crystallization and preliminary crystallographic analysis of the phosphoglycerate kinase fromAcinetobacter baumannii

2012 ◽  
Vol 68 (7) ◽  
pp. 790-792
Author(s):  
Kayla Baretta ◽  
Craig Garen ◽  
Jiang Yin ◽  
Michael N. G. James
Keyword(s):  
Synchrotron Radiation ◽  
Acinetobacter Baumannii ◽  
Light Source ◽  
Phosphoglycerate Kinase ◽  
Multidrug Resistant ◽  
Crystallographic Analysis ◽  
Lithium Sulfate ◽  
Space Group ◽  
Antibiotic Development ◽  
Potential Target

Acinetobacter baumanniiis a common multidrug-resistant clinical pathogen that is often found in hospitals. TheA. baumanniiphosphoglycerate kinase (AbPGK) is involved in the key energy-producing pathway of glycolysis and presents a potential target for antibiotic development.AbPGK has been expressed and purified; it was crystallized using lithium sulfate as the precipitant. TheAbPGK crystals belonged to space groupP2221. They diffracted to a resolution of 2.5 Å using synchrotron radiation at the Canadian Light Source.

On the Possible Spatial Structures of the β – Amyloid.

2022 ◽  
Vol 7 (1) ◽  
pp. 0-0
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Spatial Structure ◽  
Spatial Models ◽  
Globular Proteins ◽  
Spatial Structures ◽  
Higher Dimensional ◽  
Protein Molecules ◽  
Β Amyloid ◽  
First Time

Spatial models of the β - structures of protein molecules, forming layers of amino acids, in principle, of unlimited length for both antiparallel and parallel conformation have been constructed. It is shown that the simplified flat Pauling models do not reflect the spatial structure of these layers. Using the recently developed theory of higher-dimensional polytopic prismahedrons, models of the volumetric filling of space with amino acid molecules are constructed. The constructed models for the first time mathematically describe the native structures of globular proteins.

Electron Diffraction Study of α-AlMnSi Crystals Along Non-Crystallographic Zone Axes

1998 ◽  
Vol 12 (22) ◽  
pp. 2279-2303 ◽  
Author(s):  
G. L. Song ◽  
L. A. Bursill
Keyword(s):  
Electron Diffraction ◽  
Significant Proportion ◽  
Group Symmetry ◽  
Structural Basis ◽  
Quasicrystalline Phase ◽  
Thickness Variation ◽  
Crystal Thickness ◽  
Space Group Symmetry ◽  
Space Group ◽  
Diffraction Patterns

The structure of crystalline α-AlMnSi is examined by electron diffraction. Six distinct zone axes are examined, including both normal crystallographic and non-crystallographic zone axes, allowing the space group symmetry of α-AlMnSi to be studied. A method for indexing the non-crystallographic zone axis diffraction patterns, which involve reflections from several nearby crystallographic zone axes, is described and applied to electron diffraction patterns of the quasi-5-fold, 3-fold and 2-fold axes of the icosahedral building units of cubic α-AlMnSi. These are compared with electron diffraction patterns from the corresponding 5-fold, 3-fold and 2-fold axes of the quasicrystalline phase i-AlMnSi, from which we may make some conclusions concerning the occupancies of the icosahedral units in i-AlMnSi. Electron diffraction patterns characteristic of [Formula: see text] were obtained for thicker specimens. However, for thin specimens, as used for HRTEM imaging, the electron diffraction patterns were characteristic of [Formula: see text] space group symmetry. This unusual behaviour arises because the structural basis for the [Formula: see text] to [Formula: see text] phase transition is a weak effect, involving changes in occupancy of the icosahedral structural elements located at the corners (double-MacKay icosahedra) and body-centers (MacKay icosahedra) of the cubic unit cell. The effects of changing the occupancies of the outer shells of the MI and DMI structural units on the diffraction intensities of the weak reflections were examined. Thus, calculation of the dynamical diffraction amplitudes shows that in fact the weak reflections characteristic of [Formula: see text] only develop sufficient intensity if two conditions are satisfied: namely (1) the crystal thickness exceeds approx. 50 nm and (2) if a significant proportion of [Formula: see text] occupancies are included in the structural model. By fitting the observed thickness variation of the diffraction intensities we propose a new set of occupancies for α-AlMnSi, which is consistent with the electron, X-ray and neutron diffraction data.

scholarly journals Biochemical and Structural Insights into Xylan Utilization by the Thermophilic Bacterium Caldanaerobius polysaccharolyticus

2012 ◽  
Vol 287 (42) ◽  
pp. 34946-34960 ◽  
Author(s):  
Yejun Han ◽  
Vinayak Agarwal ◽  
Dylan Dodd ◽  
Jason Kim ◽  
Brian Bae ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Gene Cluster ◽  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermophilic Bacterium ◽  
Pentose Phosphate ◽  
Structural Basis ◽  
Resolution Analysis ◽  
Calorimetric Studies ◽  
Hydrolysis Of

Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.

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