scholarly journals Purification, crystallization and preliminary X-ray crystallographic studies of FMN-bound and FMN-free forms of aromatic acid decarboxylase (CpsUbiX) from the psychrophilic bacteriumColwellia psychrerythraea34H

2014 ◽  
Vol 70 (2) ◽  
pp. 215-220 ◽  
Author(s):  
Hackwon Do ◽  
Chang Woo Lee ◽  
Se Jong Han ◽  
Sung Gu Lee ◽  
Hak Jun Kim ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Aromatic Acid ◽  
Diffusion Method ◽  
Flavin Mononucleotide ◽  
Acid Decarboxylase ◽  
Data Sets ◽  
Single Mutation ◽  
Homologous Proteins ◽  
Space Group

TheubiXgene (UniProtKB code Q489U8) ofColwellia psychrerythraeastrain 34H has been annotated as a putative flavin mononucleotide (FMN)-dependent aromatic acid decarboxylase. Based on previous studies of homologous proteins, CpsUbiX is thought to catalyze the decarboxylation of 3-octaprenyl-4-hydroxybenzoate to produce 2-polyprenylphenol in the ubiquinone-biosynthesis pathway using a noncovalently bound FMN molecule as a cofactor. However, the detailed mechanisms of this important enzyme are not yet clear and need to be further elucidated. In this study, it was found that the V47S single mutation resulted in a loss of FMN binding, resulting in the production of FMN-free CpsUbiX protein. This mutation is likely to destabilize FMN–protein interactions without affecting the overall structural folding. To fully characterize the conformational changes upon FMN binding and the enzymatic mechanism at the molecular level, the wild-type (FMN-bound) and V47S mutant (FMN-free) CpsUbiX proteins were purified and crystallized using the sitting-drop vapour-diffusion method. Furthermore, complete diffraction data sets for FMN-bound (space groupC2221) and FMN-free (space groupP23) forms were obtained to 2.0 and 1.76 Å resolution, respectively.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

scholarly journals E3 Ubiquitin Ligase SPL2 Is a Lanthanide-Binding Protein

2021 ◽  
Vol 22 (11) ◽  
pp. 5712
Author(s):  
Michał Tracz ◽  
Ireneusz Górniak ◽  
Andrzej Szczepaniak ◽  
Wojciech Białek
Keyword(s):  
Ubiquitin Ligase ◽  
Conformational Changes ◽  
Protein Interactions ◽  
E3 Ubiquitin Ligase ◽  
Lanthanide Ions ◽  
E3 Ligases ◽  
Fluorescence Measurements ◽  
Partial Unfolding

The SPL2 protein is an E3 ubiquitin ligase of unknown function. It is one of only three types of E3 ligases found in the outer membrane of plant chloroplasts. In this study, we show that the cytosolic fragment of SPL2 binds lanthanide ions, as evidenced by fluorescence measurements and circular dichroism spectroscopy. We also report that SPL2 undergoes conformational changes upon binding of both Ca2+ and La3+, as evidenced by its partial unfolding. However, these structural rearrangements do not interfere with SPL2 enzymatic activity, as the protein retains its ability to auto-ubiquitinate in vitro. The possible applications of lanthanide-based probes to identify protein interactions in vivo are also discussed. Taken together, the results of this study reveal that the SPL2 protein contains a lanthanide-binding site, showing for the first time that at least some E3 ubiquitin ligases are also capable of binding lanthanide ions.

scholarly journals Detection of Protein-Protein Interactions in the Alkanesulfonate Monooxygenase System from Escherichia coli

2006 ◽  
Vol 188 (23) ◽  
pp. 8153-8159 ◽  
Author(s):  
Kholis Abdurachim ◽  
Holly R. Ellis
Keyword(s):  
Circular Dichroism ◽  
Protein Interactions ◽  
Visible Region ◽  
Circular Dichroism Spectroscopy ◽  
Flavin Mononucleotide ◽  
Stable Complex ◽  
Monooxygenase System ◽  
Protein Protein Interactions ◽  
Alkanesulfonate Monooxygenase ◽  
Circular Dichroïsm

ABSTRACT The two-component alkanesulfonate monooxygenase system utilizes reduced flavin as a substrate to catalyze a unique desulfonation reaction during times of sulfur starvation. The importance of protein-protein interactions in the mechanism of flavin transfer was analyzed in these studies. The results from affinity chromatography and cross-linking experiments support the formation of a stable complex between the flavin mononucleotide (FMN) reductase (SsuE) and monooxygenase (SsuD). Interactions between the two proteins do not lead to overall conformational changes in protein structure, as indicated by the results from circular dichroism spectroscopy in the far-UV region. However, subtle changes in the flavin environment of FMN-bound SsuE that occur in the presence of SsuD were identified by circular dichroism spectroscopy in the visible region. These data are supported by the results from fluorescent spectroscopy experiments, where a dissociation constant of 0.0022 ± 0.0010 μM was obtained for the binding of SsuE to SsuD. Based on these studies, the stoichiometry for protein-protein interactions is proposed to involve a 1:1 monomeric association of SsuE with SsuD.

scholarly journals Crystallization and preliminary X-ray analysis of formate oxidase, an enzyme of the glucose–methanol–choline oxidoreductase family

2010 ◽  
Vol 66 (9) ◽  
pp. 1064-1066 ◽  
Author(s):  
Yoshifumi Maeda ◽  
Daiju Doubayashi ◽  
Takumi Ootake ◽  
Masaya Oki ◽  
Bunzo Mikami ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Hydrogen Peroxide ◽  
Single Crystal ◽  
Aspergillus Oryzae ◽  
Diffraction Data ◽  
Diffusion Method ◽  
Hanging Drop ◽  
Space Group ◽  
X Ray ◽  
Vapour Diffusion

Formate oxidase (FOD), which catalyzes the oxidation of formate to yield carbon dioxide and hydrogen peroxide, belongs to the glucose–methanol–choline oxidoreductase (GMCO) family. FOD fromAspergillus oryzaeRIB40, which has a modified FAD as a cofactor, was crystallized at 293 K by the hanging-drop vapour-diffusion method. The crystal was orthorhombic and belonged to space groupC2221. Diffraction data were collected from a single crystal to 2.4 Å resolution.

scholarly journals POT1-TPP1 differentially regulates telomerase via POT1 His266 and as a function of single-stranded telomere DNA length

2019 ◽  
Vol 116 (47) ◽  
pp. 23527-23533 ◽  
Author(s):  
Mengyuan Xu ◽  
Janna Kiselar ◽  
Tawna L. Whited ◽  
Wilnelly Hernandez-Sanchez ◽  
Derek J. Taylor
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Environmental Changes ◽  
Lymphocytic Leukemia ◽  
Protein Protein Interactions ◽  
Cellular Environment ◽  
Multiple Protein ◽  
Linear Chromosomes ◽  
Hydroxyl Radical Footprinting ◽  
Regulate Telomere Length

Telomeres cap the ends of linear chromosomes and terminate in a single-stranded DNA (ssDNA) overhang recognized by POT1-TPP1 heterodimers to help regulate telomere length homeostasis. Here hydroxyl radical footprinting coupled with mass spectrometry was employed to probe protein–protein interactions and conformational changes involved in the assembly of telomere ssDNA substrates of differing lengths bound by POT1-TPP1 heterodimers. Our data identified environmental changes surrounding residue histidine 266 of POT1 that were dependent on telomere ssDNA substrate length. We further determined that the chronic lymphocytic leukemia-associated H266L substitution significantly reduced POT1-TPP1 binding to short ssDNA substrates; however, it only moderately impaired the heterodimer binding to long ssDNA substrates containing multiple protein binding sites. Additionally, we identified a telomerase inhibitory role when several native POT1-TPP1 proteins coat physiologically relevant lengths of telomere ssDNA. This POT1-TPP1 complex-mediated inhibition of telomerase is abrogated in the context of the POT1 H266L mutation, which leads to telomere overextension in a malignant cellular environment.

Quantitative analysis of the interactions between HIV-1 integrase and retroviral reverse transcriptases

2008 ◽  
Vol 412 (1) ◽  
pp. 163-170 ◽  
Author(s):  
Alon Herschhorn ◽  
Iris Oz-Gleenberg ◽  
Amnon Hizi
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Reaction Model ◽  
Protein Protein Interactions ◽  
Common Site ◽  
Leukaemia Virus ◽  
Reverse Transcriptases ◽  
Interaction Kinetics ◽  
Hiv 1

The RT (reverse transcriptase) of HIV-1 interacts with HIV-1 IN (integrase) and inhibits its enzymatic activities. However, the molecular mechanisms underling these interactions are not well understood. In order to study these mechanisms, we have analysed the interactions of HIV-1 IN with HIV-1 RT and with two other related RTs: those of HIV-2 and MLV (murine-leukaemia virus). All three RTs inhibited HIV-1 IN, albeit to a different extent, suggesting a common site of binding that could be slightly modified for each one of the studied RTs. Using surface plasmon resonance technology, which monitors direct protein–protein interactions, we performed kinetic analyses of the binding of HIV-1 IN to these three RTs and observed interesting binding patterns. The interaction of HIV-1 RT with HIV-1 IN was unique and followed a two-state reaction model. According to this model, the initial IN–RT complex formation was followed by a conformational change in the complex that led to an elevation of the total affinity between these two proteins. In contrast, HIV-2 and MLV RTs interacted with IN in a simple bi-molecular manner, without any apparent secondary conformational changes. Interestingly, HIV-1 and HIV-2 RTs were the most efficient inhibitors of HIV-1 IN activity, whereas HIV-1 and MLV RTs showed the highest affinity towards HIV-1 IN. These modes of direct protein interactions, along with the apparent rate constants calculated and the correlations of the interaction kinetics with the capacity of the RTs to inhibit IN activities, are all discussed.

Anion-directed assembly of lanthanide coordination polymers with SMMs properties based on a dihydrazone ligand

2018 ◽  
Vol 233 (1) ◽  
pp. 51-59
Author(s):  
Lina Zhang ◽  
Peigao Duan ◽  
Yang Liu ◽  
Jingxian Sun ◽  
Dan Zhao ◽  
...  
Keyword(s):  
Coordination Polymers ◽  
Single Molecule ◽  
Variable Temperature ◽  
Ac Susceptibility ◽  
Directed Assembly ◽  
Magnetization Measurement ◽  
Vital Role ◽  
Diffusion Method ◽  
Monoclinic Space Group ◽  
Space Group

AbstractFour new Ln(III)-based coordination polymers (CPs), [Eu(HL)Cl2(DMF)2]·(H2L) (1), [Dy(HL)Cl2(DMF)2]·(H2L) (2), [Er(HL)Cl2(DMF)(CH3OH)]·(DMF) (3) and [Yb(HL)Cl2(DMF)(H2O)]·(DMF) (4) (H2L=2,6-bis[(3-methoxysalicylidene)hydrazinocarbonyl]pyridine) have been synthesized through the reaction of Ln(III) chloride and H2L by using the vapour diffusion method. Interestingly, Cl−as a template agent plays a vital role in the formation of the target complexes. Single-crystal X-ray diffraction studies indicate that1and2are isostructural and crystallize in triclinic space groupP1̅, while complexes3and4are isostructural and crystallize in monoclinic space groupC2/c. Variable temperature magnetization measurement (χMT–T) demonstrates possible antiferromagnetic interactions in complex2. Alternating-current (ac) susceptibility measurement furthermore indicated frequency dependence for both the in-phase (χ′) and out-of-phase (χ″) components in2, suggesting that there is a slow relaxation behavior of the magnetization, which is typical of single-molecule magnets (SMMs). This is the first time that Ln(III) CPs based on such a dihydrazone ligand has been reported so far.

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