scholarly journals Pectinolytic lyases: a comprehensive review of sources, category, property, structure, and catalytic mechanism of pectate lyases and pectin lyases

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ling Zheng ◽  
Yinxiao Xu ◽  
Qian Li ◽  
Benwei Zhu
Keyword(s):  
Textile Industry ◽  
High Efficiency ◽  
Catalytic Mechanism ◽  
Three Dimensional ◽  
Relevant Information ◽  
Biochemical Properties ◽  
Dimensional Structure ◽  
Pectate Lyases ◽  
Category Property ◽  
Pectin Lyases

AbstractPectate lyases and pectin lyases have essential roles in various biotechnological applications, such as textile industry, paper making, pectic wastewater pretreatment, juice clarification and oil extraction. They can effectively cleave the α-1,4-glycosidic bond of pectin molecules back bone by β-elimination reaction to produce pectin oligosaccharides. In this way, it will not generate highly toxic methanol and has the advantages of good enzymatic selectivity, less by-products, mild reaction conditions and high efficiency. However, numerous researches have been done for several decades; there are still no comprehensive reviews to summarize the recent advances of pectate lyases and pectin lyases. This review tries to fill this gap by providing all relevant information, including the substrate, origin, biochemical properties, sequence analysis, mode of action, the three-dimensional structure and catalytic mechanism.

The first crystal structure of the peptidase domain of the U32 peptidase family

2015 ◽  
Vol 71 (12) ◽  
pp. 2505-2512 ◽  
Author(s):  
Magdalena Schacherl ◽  
Angelika A. M. Montada ◽  
Elena Brunstein ◽  
Ulrich Baumann
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Quaternary Structure ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Zinc Ion ◽  
Crystal Structure Analysis ◽  
Dimensional Structure ◽  
Sequence Motifs ◽  
Conserved Sequence

The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins fromHelicobacterandSalmonella. The first crystal structure analysis of a U32 catalytic domain fromMethanopyrus kandleri(genemk0906) reveals a modified (βα)8TIM-barrel fold with some unique features. The connecting segment between strands β7 and β8 is extended and helix α7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the β-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to aStrep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands.

Substitution of murine ferrochelatase glutamate-287 with glutamine or alanine leads to porphyrin substrate-bound variants

2001 ◽  
Vol 356 (1) ◽  
pp. 217-222 ◽  
Author(s):  
Ricardo FRANCO ◽  
Alice S. PEREIRA ◽  
Pedro TAVARES ◽  
Arianna MANGRAVITA ◽  
Michael J. BARBER ◽  
...  
Keyword(s):  
Absorption Spectra ◽  
Catalytic Mechanism ◽  
Protoporphyrin Ix ◽  
Three Dimensional ◽  
Iron Chelation ◽  
Enzymic Activity ◽  
Dimensional Structure ◽  
Wild Type ◽  
Wild Type Enzyme ◽  
Flow Experiments

Ferrochelatase (EC 4.99.1.1) is the terminal enzyme of the haem biosynthetic pathway and catalyses iron chelation into the protoporphyrin IX ring. Glutamate-287 (E287) of murine mature ferrochelatase is a conserved residue in all known sequences of ferrochelatase, is present at the active site of the enzyme, as inferred from the Bacillus subtilis ferrochelatase three-dimensional structure, and is critical for enzyme activity. Substitution of E287 with either glutamine (Q) or alanine (A) yielded variants with lower enzymic activity than that of the wild-type ferrochelatase and with different absorption spectra from the wild-type enzyme. In contrast to the wild-type enzyme, the absorption spectra of the variants indicate that these enzymes, as purified, contain protoporphyrin IX. Identification and quantification of the porphyrin bound to the E287-directed variants indicate that approx. 80% of the total porphyrin corresponds to protoporphyrin IX. Significantly, rapid stopped-flow experiments of the E287A and E287Q variants demonstrate that reaction with Zn2+ results in the formation of bound Zn-protoporphyrin IX, indicating that the endogenously bound protoporphyrin IX can be used as a substrate. Taken together, these findings suggest that the structural strain imposed by ferrochelatase on the porphyrin substrate as a critical step in the enzyme catalytic mechanism is also accomplished by the E287A and E287Q variants, but without the release of the product. Thus E287 in murine ferrochelatase appears to be critical for the catalytic process by controlling the release of the product.

On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase

1981 ◽  
Vol 293 (1063) ◽  
pp. 159-171 ◽  
Keyword(s):  
Catalytic Mechanism ◽  
Polypeptide Chain ◽  
Three Dimensional ◽  
Triose Phosphate Isomerase ◽  
Dimensional Structure ◽  
Dihydroxyacetone Phosphate ◽  
Triose Phosphate ◽  
Independent Determination ◽  
Chicken Muscle

Triose phosphate isomerase is a dimeric enzyme of molecular mass 56000 which catalyses the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde-3-phosphate. The crystal structure of the enzyme from chicken muscle has been determined at a resolution of 2.5 A, and an independent determination of the structure of the yeast enzyme has just been completed at 3 A resolution. The conformation of the polypeptide chain is essentially identical in the two structures, and consists of an inner cylinder of eight strands of parallel |3-pleated sheet, with mostly helical segments connecting each strand. The active site is a pocket containing glutamic acid 165, which is believed to act as a base in the reaction. Crystallographic studies of the binding of DHAP to both the chicken and the yeast enzymes reveal a common mode of binding and suggest a mechanism for catalysis involving polarization of the substrate carbonyl group.

scholarly journals Aptamers and Cancer

2016 ◽  
Vol 1 (1) ◽  
pp. 3
Author(s):  
Nasrin Yazdanpanahi ◽  
Mehrdad Hashemi ◽  
Abolfazl Movafagh
Keyword(s):  
Nucleotide Sequence ◽  
High Efficiency ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Target Molecule ◽  
Dna And Rna ◽  
Specific Proteins

Oligonucleotides Aptamers are single strands of DNA and RNA with the length of 20-100 nucleotides or peptides and unique three dimensional structure that is affected by nucleotide sequence. The structure exclusively influences aptamers’ bindings with its target molecule. It reduces performance or inactivate protein and this feature is used for therapeutic purposes. In addition and through connecting to signature molecule, aptamers are used to detect specific proteins. High efficiency of aptamer technology makes them a valuable tool for diagnosing and treating different diseases including cancer. The present study is an attempt to review recent studies in this field.

scholarly journals THE FRACTAL DIMENSION-BASED DESCRIPTOR OF THE MICROVASCULAR PATTERN ON THE HISTOLOGICAL SECTION

2020 ◽  
Vol 49 (3) ◽  
pp. 83-86
Author(s):  
Jaromír Šrámek ◽  
Aneta Pierzynová ◽  
Tomáš Kučera
Keyword(s):  
Fractal Dimension ◽  
Three Dimensional ◽  
Histological Section ◽  
Relevant Information ◽  
Dimensional Structure ◽  
Point Pattern ◽  
Independent Analysis ◽  
Ramp Function ◽  
Histological Processing ◽  
Microvascular Pattern

The microvascular pattern in the histological section, i.e. the point-pattern composed of capillaries perpendicular to the plane of section, contains information about the three-dimensional structure of the capillary network. Histological processing is followed by the shrinkage of tissue of uncertain magnitude. In order to obtain relevant information, the scale-independent analysis is necessary. We used an approach based on the Minkowski cover of measured set. The true fractal dimension of the point pattern is obviously of zero, but the artificial result of the algorithm can be related to the complexity of shape. We fitted the log-log plot by the modified rounded ramp function and the slope of the oblique part was used as the fractal based descriptor. We demonstrated on histological samples of the heart that this fractal-based parameter has the property of scale and rotation invariance.

scholarly journals Role of Pro-297 in the catalytic mechanism of sheep liver serine hydroxymethyltransferase

2000 ◽  
Vol 350 (3) ◽  
pp. 849-853 ◽  
Author(s):  
Rashmi TALWAR ◽  
Vijayapandian LEELAVATHY ◽  
Jala V. KRISHNA RAO ◽  
Naropantul APPAJI RAO ◽  
Handanahal S. SAVITHRI
Keyword(s):  
Aspartate Aminotransferase ◽  
Catalytic Mechanism ◽  
Three Dimensional ◽  
Proton Exchange ◽  
Serine Hydroxymethyltransferase ◽  
Dimensional Structure ◽  
Transamination Reaction ◽  
Reaction Specificity ◽  
High Degree

Serine hydroxymethyltransferase belongs to the α class of pyridoxal-5´-phosphate enzymes along with aspartate aminotransferase. Recent reports on the three-dimensional structure of human liver cytosolic serine hydroxymethyltransferase had suggested a high degree of similarity between the active-site geometries of the two enzymes. A comparison of the sequences of serine hydroxymethyltransferases revealed the presence of several highly conserved residues, including Pro-297. This residue is equivalent to residue Arg-292 of aspartate aminotransferase, which binds the γ-carboxy group of aspartate. In an attempt to change the reaction specificity of the hydroxymethyltransferase to that of an aminotransferase and to assign a possible reason for the conserved nature of Pro-297, it was mutated to Arg. The mutation decreased the hydroxymethyltransferase activity significantly (by 85–90%) and abolished the ability to catalyse alternative reactions, without alteration in the oligomeric structure, pyridoxal 5´-phosphate content or substrate binding. However, the concentration of the quinonoid intermediate and the extent of proton exchange was decreased considerably (by approx. 85%) corresponding to the decrease in catalytic activity. Interestingly, mutant Pro-297 Arg was unable to perform the transamination reaction with l-aspartate. All these results suggest that although Pro-297 is indirectly involved in catalysis, it might not have any role in imparting substrate specificity, unlike the similarly positioned Arg-292 in aspartate aminotransferase.

scholarly journals From the Eukaryotic Molybdenum Cofactor Biosynthesis to the Moonlighting Enzyme mARC

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3287 ◽  
Author(s):  
Manuel Tejada-Jimenez ◽  
Alejandro Chamizo-Ampudia ◽  
Victoria Calatrava ◽  
Aurora Galvan ◽  
Emilio Fernandez ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Cytochrome B5 ◽  
Three Dimensional ◽  
Reducing Power ◽  
Aldehyde Oxidase ◽  
Nitrite Reduction ◽  
Dimensional Structure ◽  
Enzymatic Reactions ◽  
Structural Mechanism ◽  
Cofactor Biosynthesis

All eukaryotic molybdenum (Mo) enzymes contain in their active site a Mo Cofactor (Moco), which is formed by a tricyclic pyranopterin with a dithiolene chelating the Mo atom. Here, the eukaryotic Moco biosynthetic pathway and the eukaryotic Moco enzymes are overviewed, including nitrate reductase (NR), sulfite oxidase, xanthine oxidoreductase, aldehyde oxidase, and the last one discovered, the moonlighting enzyme mitochondrial Amidoxime Reducing Component (mARC). The mARC enzymes catalyze the reduction of hydroxylated compounds, mostly N-hydroxylated (NHC), but as well of nitrite to nitric oxide, a second messenger. mARC shows a broad spectrum of NHC as substrates, some are prodrugs containing an amidoxime structure, some are mutagens, such as 6-hydroxylaminepurine and some others, which most probably will be discovered soon. Interestingly, all known mARC need the reducing power supplied by different partners. For the NHC reduction, mARC uses cytochrome b5 and cytochrome b5 reductase, however for the nitrite reduction, plant mARC uses NR. Despite the functional importance of mARC enzymatic reactions, the structural mechanism of its Moco-mediated catalysis is starting to be revealed. We propose and compare the mARC catalytic mechanism of nitrite versus NHC reduction. By using the recently resolved structure of a prokaryotic MOSC enzyme, from the mARC protein family, we have modeled an in silico three-dimensional structure of a eukaryotic homologue.

scholarly journals Efficient targeting to storage granules of human proinsulins with altered propeptide domain.

1988 ◽  
Vol 106 (6) ◽  
pp. 1843-1851 ◽  
Author(s):  
S K Powell ◽  
L Orci ◽  
C S Craik ◽  
H P Moore
Keyword(s):  
High Efficiency ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structural Domains ◽  
C Peptide ◽  
Three Dimensional Structure ◽  
Morphological Criteria ◽  
Cellular Machinery ◽  
Storage Granules

In neuronal and endocrine cells, peptide hormones are selectively segregated into storage granules, while other proteins are exported continuously without storage. Sorting of hormones by cellular machinery involves the recognition of specific structural domains on prohormone molecules. Since the propeptide of insulin is known to play an important role in its three-dimensional structure, it is reasonable to speculate that targeting of proinsulin to storage granules would require a functional connecting peptide. To test this hypothesis, we constructed two mutations in human proinsulin with different predicted structures. In one mutation, Ins delta C, the entire C peptide was deleted, resulting in an altered insulin in which the B and the A chains are joined contiguously. In the other mutation, Ins/IGF, the C peptide of proinsulin was replaced with the unrelated 12-amino acid connecting peptide of human insulin-like growth factor-I; this substitution should permit correct folding of the B and A chains to form a tertiary structure similar to that of proinsulin. By several biochemical and morphological criteria, we found that Ins/IGF is efficiently targeted to storage granules, suggesting that the C peptide of proinsulin does not contain necessary sorting information. Unexpectedly, Ins delta C, which presumably cannot fold properly, is also targeted to granules at a high efficiency. These results imply that either the targeting machinery can tolerate changes in the tertiary structure of transported proteins, or that the B and A chains of insulin can form a relatively intact three-dimensional structure even in the absence of C peptide.

scholarly journals Using a Three-Dimensional Reduction Method in the High-Efficiency Grain Selector and Corresponding Grain Selection Mechanism

Materials ◽  
2019 ◽  
Vol 12 (11) ◽  
pp. 1781
Author(s):  
Xintao Zhu ◽  
Fu Wang ◽  
Shuaipeng Zhang ◽  
Tobias Wittenzellner ◽  
Jessica Frieß ◽  
...  
Keyword(s):  
Single Crystal ◽  
High Efficiency ◽  
Turbine Blades ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Selection Mechanism ◽  
Dimensional Reduction Method ◽  
Optimization Parameters ◽  
Dimensional Coupling

In the development of a high-efficiency grain selector, the spiral selectors are widely used in Ni-based single crystal (SX) superalloys casting to produce single crystal turbine blades. For the complex three-dimensional structure of the spiral, a 2D grain selector was designed to investigate in this paper. As a result, the parameters of two-dimensional grain selection bond and the corresponding grain selection mechanism were established, and the three-dimensional grain selection bond was designed again by means of two-dimensional coupling optimization parameters.

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