Influence of saccharide modifications on heparin lyase III substrate specificities

Glycobiology ◽  
2021 ◽  
Author(s):  
Jiandong Wu ◽  
Pradeep Chopra ◽  
Geert-Jan Boons ◽  
Joseph Zaia
Keyword(s):  
Enzyme Activity ◽  
Structure Function ◽  
Heparan Sulfate ◽  
Chain Length ◽  
Biological Processes ◽  
Substrate Specificities ◽  
Sulfated Oligosaccharides ◽  
Flavobacterium Heparinum ◽  
Inhibited Enzyme

Abstract A library of 23 synthetic heparan sulfate (HS) oligosaccharides, varying in chain length, types, and positions of modifications, was used to analyze the substrate specificities of heparin lyase III enzymes from both Flavobacterium heparinum and Bacteroides eggerthii. The influence of specific modifications, including N-substitution, 2-O sulfation, 6-O sulfation, and 3-O sulfation on lyase III digestion was examined systematically. It was demonstrated that lyase III from both sources can completely digest oligosaccharides lacking O-sulfates. 2-O Sulfation completely blocked cleavage at the corresponding site; 6-O and 3-O sulfation on glucosamine residues inhibited enzyme activity. We also observed that there are differences in substrate specificities between the two lyase III enzymes for highly sulfated oligosaccharides. These findings will facilitate obtaining and analyzing the functional sulfated domains from large HS polymer, to better understand their structure/function relationships in biological processes.

Topological frustration leading to backtracking in a coupled folding-binding process

2021 ◽  
Author(s):  
Meng Gao ◽  
Ping Li ◽  
Zhengding Su ◽  
Yongqi Huang
Keyword(s):  
Structure Function ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Biological Processes ◽  
Sequence Structure ◽  
Binding Process ◽  
Intrinsically Disordered

Intrinsically disordered proteins (IDPs) are abundant in all species. Their discovery challenges the traditional “sequence−structure−function” paradigm of protein science, because IDPs play important roles in various biological processes without preformed...

Phosphatase systems in Fasciolopsis buski Lankester, 1857 and Gastrodiscus aegyptiacus Cobbold, 1876

Parasitology ◽  
1973 ◽  
Vol 67 (2) ◽  
pp. 197-204 ◽  
Author(s):  
Madan M. Goil
Keyword(s):  
Enzyme Activity ◽  
Tartaric Acid ◽  
Maximum Activity ◽  
Nitrophenyl Phosphate ◽  
Biochemical Studies ◽  
Phosphate Hydrolysis ◽  
Fasciolopsis Buski ◽  
Enzyme I ◽  
Inhibited Enzyme ◽  
Acid Phosphomonoesterase

Biochemical studies on the non-specific phosphomonoesterases have demonstrated the presence of acid phosphomonoesterase with maximum activity at pH 4·0 in Gastrodiscus aegyptiacus (enzyme I) and at pH 4·5 in the case of Fasdolopsis buski (enzyme II). The Km for ρ-nitrophenyl phosphate hydrolysis was 0·66 mM for enzyme I and 1·1 mM for enzyme II. Different concentrations of fluoride, arsenate, tartrate, tartaric acid, cysteine and copper brought about inhibition of both enzymes and magnesium, iodoaeetate, iodoacetamide and EDTA had no influence on either enzyme activity. Cobalt activated both enzymes while zinc inhibited enzyme I and strongly stimulated enzyme II.

Coenzyme A metabolism

1985 ◽  
Vol 248 (1) ◽  
pp. E1-E9 ◽  
Author(s):  
J. D. Robishaw ◽  
J. R. Neely
Keyword(s):  
Enzyme Activity ◽  
Cardiac Muscle ◽  
Heart Muscle ◽  
Coenzyme A ◽  
Free Carnitine ◽  
Pantothenate Kinase ◽  
Acetyl Coenzyme A ◽  
Synthetic Pathway ◽  
And Control ◽  
Inhibited Enzyme

The metabolism of coenzyme A and control of its synthesis are reviewed. Pantothenate kinase is an important rate-controlling enzyme in the synthetic pathway of all tissues studied and appears to catalyze the flux-generating reaction of the pathway in cardiac muscle. This enzyme is strongly inhibited by coenzyme A and all of its acyl esters. The cytosolic concentrations of coenzyme A and acetyl coenzyme A in both liver and heart are high enough to totally inhibit pantothenate kinase under all conditions. Free carnitine, but not acetyl carnitine, deinhibits the coenzyme A-inhibited enzyme. Carnitine alone does not increase enzyme activity. Thus changes in the acetyl carnitine-to-carnitine ratio that occur with nutritional states provides a mechanism for regulation of coenzyme A synthetic rates. Changes in the rate of coenzyme A synthesis in liver and heart occurs with fasting, refeeding, and diabetes and in heart muscle with hypertrophy. The pathway and regulation of coenzyme A degradation are not understood.

scholarly journals Distinct glycosaminoglycan chain length and sulfation patterns required for cellular uptake of Tau, Aβ, and α-Synuclein

2017 ◽  
Author(s):  
Barbara E. Stopschinski ◽  
Brandon B. Holmes ◽  
Gregory M. Miller ◽  
Jaime Vaquer-Alicea ◽  
Linda C. Hsieh-Wilson ◽  
...  
Keyword(s):  
Cell Surface ◽  
Neurodegenerative Diseases ◽  
Heparan Sulfate ◽  
Chain Length ◽  
Cellular Uptake ◽  
Genetic Manipulation ◽  
Heparan Sulfate Proteoglycans ◽  
Cell Uptake ◽  
Major Genes

AbstractTranscellular propagation of aggregate “seeds” has been proposed to mediate progression of neurodegenerative diseases in tauopathies and α-synucleinopathies. We have previously determined that tau and α-synuclein aggregates bind heparan sulfate proteoglycans (HSPGs) on the cell surface. This mediates uptake and intracellular seeding. The specificity and mode of binding to HSPGs has been unknown. We used modified heparins to determine the size and sulfation requirements of glycosaminoglycan (GAGs) binding to aggregates in biochemical and cell uptake and seeding assays. Aggregates of tau require a precise GAG architecture with defined sulfate moieties in the N- and 6-O-positions, whereas α-synuclein and Aβ rely slightly more on overall charge on the GAGs. To determine the genetic requirements for aggregate uptake, we individually knocked out the major genes of the HSPG synthesis pathway using CRISPR/Cas9 in HEK293T cells. Knockout of EXT1, EXT2 and EXTL3, N-sulfotransferase (NDST1), and 6-O-sulfotransferase (HS6ST2) significantly reduced tau uptake. α-Synuclein was not sensitive to HS6ST2 knockout. Good correlation between pharmacologic and genetic manipulation of GAG binding by tau and α-synuclein indicates specificity that may help elucidate a path to mechanism-based inhibition of transcellular propagation of pathology.

scholarly journals New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships

2014 ◽  
Vol 289 (44) ◽  
pp. 30221-30228 ◽  
Author(s):  
Shoshana D. Brown ◽  
Patricia C. Babbitt
Keyword(s):  
Structure Function ◽  
Active Sites ◽  
Large Scale ◽  
Common Ancestor ◽  
Enzyme Evolution ◽  
Large Set ◽  
Substrate Specificities ◽  
Functionally Diverse

Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes.

Structure-function relationship of substrate length specificity of dextran glucosidase from Streptococcus mutans

Biologia ◽  
2008 ◽  
Vol 63 (6) ◽  
Author(s):  
Wataru Saburi ◽  
Hironori Hondoh ◽  
Young-Min Kim ◽  
Haruhide Mori ◽  
Masayuki Okuyama ◽  
...  
Keyword(s):  
Structure Function ◽  
High Activity ◽  
Streptococcus Mutans ◽  
Chain Length ◽  
Structural Elements ◽  
Chain Length Specificity ◽  
Structure Function Relationship ◽  
Function Relationship ◽  
Relationship Of ◽  
Long Chain

AbstractDextran glucosidase from Streptococcus mutans (SMDG), an exo-type glucosidase of glycoside hydrolase (GH) family 13, specifically hydrolyzes an α-1,6-glucosidic linkage at the non-reducing ends of isomaltooligosaccharides and dextran. SMDG shows the highest sequence similarity to oligo-1,6-glucosidases (O16Gs) among GH family 13 enzymes, but these enzymes are obviously different in terms of substrate chain length specificity. SMDG efficiently hydrolyzes both short-and long-chain substrates, while O16G acts on only short-chain substrates. We focused on this difference in substrate specificity between SMDG and O16G, and elucidated the structure-function relationship of substrate chain length specificity in SMDG. Crystal structure analysis revealed that SMDG consists of three domains, A, B, and C, which are commonly found in other GH family 13 enzymes. The structural comparison between SMDG and O16G from Bacillus cereus indicated that Trp238, spanning subsites +1 and +2, and short β → α loop 4, are characteristic of SMDG, and these structural elements are predicted to be important for high activity toward long-chain substrates. The substrate size preference of SMDG was kinetically analyzed using two mutants: (i) Trp238 was replaced by a smaller amino acid, alanine, asparagine or proline; and (ii) short β → α loop 4 was exchanged with the corresponding loop of O16G. Mutant enzymes showed lower preference for long-chain substrates than wild-type enzyme, indicating that these structural elements are essential for the high activity toward long-chain substrates, as implied by structural analysis.

Pseudoproteases: mechanisms and function

2015 ◽  
Vol 468 (1) ◽  
pp. 17-24 ◽  
Author(s):  
Simone L. Reynolds ◽  
Katja Fischer
Keyword(s):  
Structure Function ◽  
Mode Of Action ◽  
Immune Modulation ◽  
Therapeutic Targets ◽  
Structure Functions ◽  
Present Review ◽  
Biological Processes ◽  
And Function ◽  
Classification Structure

Catalytically inactive enzymes (also known as pseudoproteases, protease homologues or paralogues, non-peptidase homologues, non-enzymes and pseudoenzymes) have traditionally been hypothesized to act as regulators of their active homologues. However, those that have been characterized demonstrate that inactive enzymes have an extensive and expanding role in biological processes, including regulation, inhibition and immune modulation. With the emergence of each new genome, more inactive enzymes are being identified, and their abundance and potential as therapeutic targets has been realized. In the light of the growing interest in this emerging field the present review focuses on the classification, structure, function and mechanism of inactive enzymes. Examples of how inactivity is defined, how this is reflected in the structure, functions of inactive enzymes in biological processes and their mode of action are discussed.

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