A novel GH13 subfamily of α-amylases with a pair of tryptophans in the helix α3 of the catalytic TIM-barrel, the LPDlx signature in the conserved sequence region V and a conserved aromatic motif at the C-terminus

Biologia ◽  
2015 ◽  
Vol 70 (10) ◽  
Author(s):  
Štefan Janeček ◽  
Andrea Kuchtová ◽  
Soňa Petrovičová
Keyword(s):  
Structural Features ◽  
Point Of View ◽  
Enzyme Specificity ◽  
Entire Family ◽  
Amylolytic Enzymes ◽  
Conserved Sequence ◽  
C Terminus ◽  
Cazy Database ◽  
Tim Barrel ◽  
Evolutionary Comparison

AbstractThe α-amylase enzyme specificity has been classified in the Carbohydrate-Active enZyme (CAZy) database into the families GH13, GH57, GH119 and eventually also GH126. α-Amylase is a glycoside hydrolase (GH) that catalyses in an endo-fashion the hydrolysis of the α-1,4-glucosidic linkages in starch and related α-glucans employing the retaining reaction mechanism. The family GH13 is the main α-amylase family with more than 28,000 members and 30 different specificities. The entire family GH13 has already been divided into 40 subfamilies; the α-amylase enzyme specificity being found in the subfamilies GH13 1, 5, 6, 7, 15, 19, 24, 27, 28, 32, 36 and 37. The present in silico study delivers a proposal to create a novel GH13 subfamily with the specificity of α-amylase. The proposal is based on a detailed bioinformatics analysis consisting of sequence, structural and evolutionary comparison of experimentally characterized α-amylases from, e.g., Bacillus aquimaris, Anoxybacillus sp. SK3-4 and DT3-1 and Geobacillus thermoleovorans, and hypothetical proteins, accompanied by α-amylases from well-established GH13 subfamilies and by closely related amylolytic enzymes (mainly from the subfamily GH13 31). Three sequence-structural features can be ascribed to the members of the newly proposed GH13 subfamily: (i) the pair of adjacent tryptophan residues positioned between the CSR-V and CSR-II in the helix α3 of the catalytic TIM-barrel; (ii) the sequence LPDlx in their CSR-V; and (iii) a ~30-residue long C-terminal region with a motif of five conserved aromatic residues. From the evolutionary point of view, the novel GH13 α-amylase subfamily is most closely related to fungal and yeast α-amylases classified in the subfamily GH13_1.

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.

THE USE OF THE TRANSLATION METHOD IN MASTERING THE TERMS

2019 ◽  
pp. 87-95
Keyword(s):  
International Relations ◽  
English Language ◽  
Structural Features ◽  
Point Of View ◽  
General Classification ◽  
Optimal Methods ◽  
Foreign Companies ◽  
The Social ◽  
Problems Of Translation

The article is devoted to the role of Tourism terminology in linguistics and the issue of general classification, peculiarities in the expression and translation of terms related to tourism in English into Uzbek and Russian, as well as the choice of the most optimal methods for translating terms in accordance with the requirements of this professional sphere. The terminology of the English language tourism is distinguished by its brightness, versatility. Tourism terms are formed under the influence of a generalized lexical layer of language and perform a specific functional function.Tourism terms are formed through the affixation method (prefixation, suffixation, circumphixation) and get rich through the process.The terminology of English Tourism is distinguished by its content and structural features, forming a part of the language vocabulary from the linguistic point of view. Texts in the field of Tourism take into their composition concepts of Tourism and interpret them in their content. They will be mainly in the form of advertising, as well as enlighten information about a particular region or place, create informational precedents and ensure their manifestation in the social cultural presence. The relevance of the study of the problems of translation of terms in the field of tourism has been investigated, mainly due to the development of international relations, expansion of cooperation between local and foreign companies, as well as the increase in this area of communication.

Purification and Characterization of Natural Solid-Substrate Degrading and Alcohol Producing Hyperthermostable Alkaline Amylase from Bacillus cereus (sm-sr14)

2020 ◽  
Vol 21 (9) ◽  
pp. 872-881
Author(s):  
Sumit Sahoo ◽  
Sudipta Roy ◽  
Dipannita Santra ◽  
Sayantani Maiti ◽  
Sonali Roul ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Main Property ◽  
Solid Substrate ◽  
Industrial Applications ◽  
Starch Degradation ◽  
Significant Similarity ◽  
Alcohol Production ◽  
Cazy Database ◽  
Tim Barrel ◽  
Alkaline Amylase

Objective: Amylases enzymes hydrolyze starch molecules to produce diverse products including dextrins, and progressively smaller polymers. These include glucose units linked through α-1- 1, α-1-4, α-1-6, glycosidic bonds. Methods: This enzyme carrying an (α /β) 8 or TIM barrel structure is also produced containing the catalytic site residues. These groups of enzymes possess four conserved regions in their primary sequence. In the Carbohydrate-Degrading Enzyme (CAZy) database, α-amylases are classified into different Glycoside Hydrolase Families (GHF) based on their amino acid sequence. The present objective was to study one such enzyme based on its molecular characterization after purification in our laboratory. Its main property of solid-natural starch degradation was extensively investigated for its pharmaceutical/ industrial applications. Results: Amylase producing bacteria Bacillus cereus sm-sr14 (Accession no. KM251578.1) was purified to homogeneity on a Seralose 6B-150 gel-matrix and gave a single peak during HPLC. MALDITOF mass-spectrometry with bioinformatics studies revealed its significant similarity to α/β hydrolase family. The enzyme showed an efficient application; favourable Km, Vmax and Kcat during the catalysis of different natural solid starch materials. Analysis for hydrolytic product showed that this enzyme can be classified as the exo-amylase asit produced a significant amount of glucose. Conclusion: Besides the purified enzyme, the present organism Bacillus cereus sm-sr14 could degrade natural solid starch materials like potato and rice up to the application level in the pharmaceutical/ industrial field for alcohol production.

A Mutation in Paramecium tetraurelia Reveals Functional and Structural Features of Developmentally Excised DNA Elements

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 139-149 ◽  
Author(s):  
Kimberly M Mayer ◽  
Kazuyuki Mikami ◽  
James D Forney
Keyword(s):  
Mutant Cell ◽  
Consensus Sequence ◽  
Surface Protein ◽  
Structural Features ◽  
Inverted Terminal Repeat ◽  
Paramecium Tetraurelia ◽  
Coding Region ◽  
Conserved Sequence ◽  
Variable Surface ◽  
Dna Elements

Abstract The excision of internal eliminated sequences (IESs) from the germline micronuclear DNA occurs during the differentiation of a new macronuclear genome in ciliated protozoa. In Paramecium, IESs are generally short (28–882 bp), AT rich DNA elements that show few conserved sequence features with the exception of an inverted-terminal-repeat consensus sequence that has similarity to the ends of mariner/Tc1 transposons (Klobutcher and Herrick 1995). We have isolated and analyzed a mutant cell line that cannot excise a 370-bp IESs (IES2591) from the coding region of the 51A variable surface protein gene. A single micronuclear C to T transition within the consensus sequence prevents excision. The inability to excise IES2591 has revealed a 28-bp IES inside the larger IES, suggesting that reiterative integration of these elements can occur. Together, the consensus sequence mutation and the evidence for reiterative integration support the theory that Paramecium IESs evolved from transposable elements. Unlike a previously studied Paramecium IES, the presence of this IES in the macronucleus does not completely inhibit excision of its wild-type micronuclear copy through multiple sexual generations.

Warm-up as part of a training session

2021 ◽  
pp. 89-98
Author(s):  
Е.И. Чучкалова ◽  
О.Г. Маскина
Keyword(s):  
Higher Education ◽  
Training Session ◽  
Practical Experience ◽  
Structural Features ◽  
Educational Process ◽  
Point Of View ◽  
Educational Organizations ◽  
Business Training ◽  
Warm Up ◽  
Teachers And Students

Статья посвящена организации учебного процесса в высшей школе. Авторы, в частности, считают, что лекционные и практические занятия должны начинаться и заканчиваться разминкой, подразумевающей выполнение коротких упражнений. С помощью специально проведенного исследования в работе анализируются структурные особенности учебных разминок, уточняются их отличия от бизнес-разминок, применяемых в ходе тренингов, а также рассматривается с содержательной и организационной точек зрения специфика применения разминок в высшей школе. Выводы сделаны с учетом мнения преподавателей и студентов, уже имеющих опыт участия в разминках. Научная новизна публикации заключается в расширении представлений о возможностях, которые открываются при использовании разминок в учебном процессе. В статье проведена их классификация по различным критериям: виду активности, массовости, желаемому результату, формату проведения. Кроме того, автор обобщил собственный практический опыт использования инструментов бизнес-тренингов, накопленный в ходе подготовки бакалавров и магистрантов, привел примеры наиболее популярных упражнений в каждой группе матрицы разминок. Особое внимание уделено разминкам, сопровождающим вебинары, что продолжает оставаться чрезвычайно актуальным в свете современного перехода на смешанный формат обучения в профессиональном образовании. Статья предназначена для преподавателей и студентов высших и средних профессиональных образовательных организаций. The article focuses on the organization of the educational process in higher education. The author, in particular, believes that lectures and practical classes should begin and end with a warm-up, which implies doing short exercises. With the help of specially conducted research, the paper analyzes the structural features of training warm-ups, clarifies their differences from business warm-ups used during training, and also considers the specifics of using warm-ups in higher education from a substantive and organizational point of view. The conclusions are made considering the opinions of teachers and students who already have experience of doing warm-ups. The scientific novelty of the publication lies in bringing better understanding of the opportunities that open up with using warm-ups in the educational process. The article classifies them according to various criteria: the type of activity, mass character, the desired result, the format of the event. In addition, the author summarized his own practical experience of using business training tools during the preparation of bachelors and undergraduates gave examples of the most popular exercises in each group of the warm-up matrix. Special attention is paid to the warm-ups accompanying webinars, which continues to be extremely relevant in the light of the modern transition to a mixed format of training in vocational education. The article is intended for teachers and students of higher and secondary professional educational organizations.

Volcanoes geological mapping and structural geology with UAS High Resolution Digital Terrain Model : the Kuei-Shan Tao case example (Eastern Taiwan).

2021 ◽  
Author(s):  
Benoit Deffontaines ◽  
Kuo-Jen Chang ◽  
Samuel Magalhaes ◽  
Gérardo Fortunato
Keyword(s):  
High Resolution ◽  
Okinawa Trough ◽  
Volcanic Rocks ◽  
Digital Terrain Model ◽  
Structural Features ◽  
Point Of View ◽  
Geological Mapping ◽  
Lava Flows ◽  
Aerial Photographs ◽  
Structural Scheme

<p>Volcanic areas in the World are often difficult to map especially in a structural point of view as (1) fault planes are generally covered and filled by more recent lava flows and (2) volcanic rocks have very few tectonic striations. Kuei-Shan Tao (11km from Ilan Plain – NE Taiwan) is a volcanic island, located at the soutwestern tip of the South Okinawa trough (SWOT). Two incompatible geological maps had been already published both lacking faults and structural features (Hsu, 1963 and Chiu et al., 2010). We propose herein not only to up-date the Kuei-Shan Tao geological map with our high resolution dataset, but also to create the Kuei-Shan Tao structural scheme in order to better understand its geological and tectonic history.</p><p>Consequently, we first acquired aerial photographs from our UAS survey and get our new UAS high resolution DTM (HR UAS-DTM hereafter) with a ground resolution <10cm processed through classical photogrammetric methods. Taking into account common sense geomorphic and structural interpretation and reasoning deduced form our HR UAS-DTM, and the outcropping lithologies situated all along the shoreline, we have up-dated the Kuei-Shan Tao geological mapping and its major structures. To conclude, the lithologies (andesitic lava flows and pyroclastic falls) and the new structural scheme lead us to propose a scenario for both the construction as well as the dismantling of Kuei-Shan Tao which are keys for both geology and geodynamics of the SWOT.</p>

Structural features of the C-terminus from the human neurokinin-1 receptor

FEBS Journal ◽  
2012 ◽  
Vol 279 (13) ◽  
pp. 2357-2367 ◽  
Author(s):  
Mikhail Orel ◽  
Esteve Padrós ◽  
Joan Manyosa
Keyword(s):  
Structural Features ◽  
Neurokinin 1 Receptor ◽  
C Terminus ◽  
Neurokinin 1

Polyadenylation of mRNA: minimal substrates and a requirement for the 2' hydroxyl of the U in AAUAAA

1990 ◽  
Vol 10 (4) ◽  
pp. 1705-1713
Author(s):  
P L Wigley ◽  
M D Sheets ◽  
D A Zarkower ◽  
M E Whitmer ◽  
M Wickens
Keyword(s):  
Cleavage Site ◽  
Structural Features ◽  
Single Nucleotide ◽  
Conserved Sequence ◽  
Specificity Factor

mRNA-specific polyadenylation can be assayed in vitro by using synthetic RNAs that end at or near the natural cleavage site. This reaction requires the highly conserved sequence AAUAAA. At least two distinct nuclear components, an AAUAAA specificity factor and poly(A) polymerase, are required to catalyze the reaction. In this study, we identified structural features of the RNA substrate that are critical for mRNA-specific polyadenylation. We found that a substrate that contained only 11 nucleotides, of which the first six were AAUAAA, underwent AAUAAA-specific polyadenylation. This is the shortest substrate we have used that supports polyadenylation: removal of a single nucleotide from either end of this RNA abolished the reaction. Although AAUAAA appeared to be the only strict sequence requirement for polyadenylation, the number of nucleotides between AAUAAA and the 3' end was critical. Substrates with seven or fewer nucleotides beyond AAUAAA received poly(A) with decreased efficiency yet still bound efficiently to specificity factor. We infer that on these shortened substrates, poly(A) polymerase cannot simultaneously contact the specificity factor bound to AAUAAA and the 3' end of the RNA. By incorporating 2'-deoxyuridine into the U of AAUAAA, we demonstrated that the 2' hydroxyl of the U in AAUAAA was required for the binding of specificity factor to the substrate and hence for poly(A) addition. This finding may indicate that at least one of the factors involved in the interaction with AAUAAA is a protein.

scholarly journals Glucoamylase starch-binding domain of Aspergillus niger B1: molecular cloning and functional characterization

2003 ◽  
Vol 372 (3) ◽  
pp. 905-910 ◽  
Author(s):  
Tzur PALDI ◽  
Ilan LEVY ◽  
Oded SHOSEYOV
Keyword(s):  
Aspergillus Niger ◽  
Corn Starch ◽  
Catalytic Domain ◽  
Functional Characterization ◽  
Carbohydrate Binding ◽  
Amylolytic Enzymes ◽  
Binding Domains ◽  
C Terminus ◽  
Carbohydrate Binding Modules ◽  
Modified Starches

Carbohydrate-binding modules (CBMs) are protein domains located within a carbohydrate-active enzyme, with a discrete fold that can be separated from the catalytic domain. Starch-binding domains (SBDs) are CBMs that are usually found at the C-terminus in many amylolytic enzymes. The SBD from Aspergillus niger B1 (CMI CC 324262) was cloned and expressed in Escherichia coli as an independent domain and the recombinant protein was purified on starch. The A. niger B1 SBD was found to be similar to SBD from A. kawachii, A. niger var. awamori and A. shirusami (95–96% identity) and was classified as a member of the CBM family 20. Characterization of SBD binding to starch indicated that it is essentially irreversible and that its affinity to cationic or anionic starch, as well as to potato or corn starch, does not differ significantly. These observations indicate that the fundamental binding area on these starches is essentially the same. Natural and chemically modified starches are among the most useful biopolymers employed in the industry. Our study demonstrates that SBD binds effectively to both anionic and cationic starch.

scholarly journals Coupled Translocation Events Generate Topological Heterogeneity at the Endoplasmic Reticulum Membrane

1998 ◽  
Vol 9 (9) ◽  
pp. 2681-2697 ◽  
Author(s):  
Kenneth Moss ◽  
Andrew Helm ◽  
Yun Lu ◽  
Alvina Bragin ◽  
William R. Skach
Keyword(s):  
Endoplasmic Reticulum ◽  
Structural Features ◽  
Endoplasmic Reticulum Membrane ◽  
Type I ◽  
Type Ii ◽  
Hydrophobic Residues ◽  
P Glycoprotein ◽  
C Terminus ◽  
Signal Anchor ◽  
Hydrophilic Residues

Topogenic determinants that direct protein topology at the endoplasmic reticulum membrane usually function with high fidelity to establish a uniform topological orientation for any given polypeptide. Here we show, however, that through the coupling of sequential translocation events, native topogenic determinants are capable of generating two alternate transmembrane structures at the endoplasmic reticulum membrane. Using defined chimeric and epitope-tagged full-length proteins, we found that topogenic activities of two C-trans (type II) signal anchor sequences, encoded within the seventh and eighth transmembrane (TM) segments of human P-glycoprotein were directly coupled by an inefficient stop transfer (ST) sequence (TM7b) contained within the C-terminus half of TM7. Remarkably, these activities enabled TM7 to achieve both a single- and a double-spanning TM topology with nearly equal efficiency. In addition, ST and C-trans signal anchor activities encoded by TM8 were tightly linked to the weak ST activity, and hence topological fate, of TM7b. This interaction enabled TM8 to span the membrane in either a type I or a type II orientation. Pleiotropic structural features contributing to this unusual topogenic behavior included 1) a short, flexible peptide loop connecting TM7a and TM7b, 2) hydrophobic residues within TM7b, and 3) hydrophilic residues between TM7b and TM8.

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