Changing the Enzymatic Activity of T7 Endonuclease by Mutations at the β-Bridge Site:  Alteration of Substrate Specificity Profile and Metal Ion Requirements by Mutation Distant from the Catalytic Domain

Biochemistry ◽  
2004 ◽  
Vol 43 (14) ◽  
pp. 4313-4322 ◽  
Author(s):  
Chudi Guan ◽  
Sanjay Kumar ◽  
Rebecca Kucera ◽  
Amy Ewel
Keyword(s):  
Substrate Specificity ◽  
Enzymatic Activity ◽  
Metal Ion ◽  
Catalytic Domain ◽  
Bridge Site

scholarly journals Arabidopsis thaliana β1,2-xylosyltransferase: an unusual glycosyltransferase with the potential to act at multiple stages of the plant N-glycosylation pathway

2005 ◽  
Vol 388 (2) ◽  
pp. 515-525 ◽  
Author(s):  
Peter BENCÚR ◽  
Herta STEINKELLNER ◽  
Barbara SVOBODA ◽  
Jan MUCHA ◽  
Richard STRASSER ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Substrate Specificity ◽  
Metal Ion ◽  
Catalytic Domain ◽  
Protein Characterization ◽  
Reaction Products ◽  
Glycosylation Sites ◽  
Glycosylation Pathway ◽  
Multiple Stages

XylT (β1,2-xylosyltransferase) is a unique Golgi-bound glycosyltransferase that is involved in the biosynthesis of glycoprotein-bound N-glycans in plants. To delineate the catalytic domain of XylT, a series of N-terminal deletion mutants was heterologously expressed in insect cells. Whereas the first 54 residues could be deleted without affecting the catalytic activity of the enzyme, removal of an additional five amino acids led to the formation of an inactive protein. Characterization of the N-glycosylation status of recombinant XylT revealed that all three potential N-glycosylation sites of the protein are occupied by N-linked oligosaccharides. However, an unglycosylated version of the enzyme displayed substantial catalytic activity, demonstrating that N-glycosylation is not essential for proper folding of XylT. In contrast with most other glycosyltransferases, XylT is enzymatically active in the absence of added metal ions. This feature is not due to any metal ion directly associated with the enzyme. The precise acceptor substrate specificity of XylT was assessed with several physiologically relevant compounds and the xylosylated reaction products were subsequently tested as substrates of other Golgi-resident glycosyltransferases. These experiments revealed that the substrate specificity of XylT permits the enzyme to act at multiple stages of the plant N-glycosylation pathway.

Structural insights into dihydroxylation of terephthalate, a product of polyethylene terephthalate degradation

2022 ◽  
Author(s):  
Jai Krishna Mahto ◽  
Neetu Neetu ◽  
Monica Sharma ◽  
Monika Dubey ◽  
Bhanu Prakash Vellanki ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Specificity ◽  
Polyethylene Terephthalate ◽  
Active Site ◽  
Catalytic Domain ◽  
Structural Features ◽  
Comamonas Testosteroni ◽  
Plastic Pollution ◽  
Microbial Utilization ◽  
Steady State Kinetics

Biodegradation of terephthalate (TPA) is a highly desired catabolic process for the bacterial utilization of this Polyethylene terephthalate (PET) depolymerization product, but to date, the structure of terephthalate dioxygenase (TPDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of TPA to a cis -diol is unavailable. In this study, we characterized the steady-state kinetics and first crystal structure of TPDO from Comamonas testosteroni KF1 (TPDO KF1 ). The TPDO KF1 exhibited the substrate specificity for TPA ( k cat / K m = 57 ± 9 mM −1 s −1 ). The TPDO KF1 structure harbors characteristics RO features as well as a unique catalytic domain that rationalizes the enzyme’s function. The docking and mutagenesis studies reveal that its substrate specificity to TPA is mediated by Arg309 and Arg390 residues, two residues positioned on opposite faces of the active site. Additionally, residue Gln300 is also proven to be crucial for the activity, its substitution to alanine decreases the activity ( k cat ) by 80%. Together, this study delineates the structural features that dictate the substrate recognition and specificity of TPDO. Importance The global plastic pollution has become the most pressing environmental issue. Recent studies on enzymes depolymerizing polyethylene terephthalate plastic into terephthalate (TPA) show some potential in tackling this. Microbial utilization of this released product, TPA is an emerging and promising strategy for waste-to-value creation. Research from the last decade has discovered terephthalate dioxygenase (TPDO), as being responsible for initiating the enzymatic degradation of TPA in a few Gram-negative and Gram-positive bacteria. Here, we have determined the crystal structure of TPDO from Comamonas testosteroni KF1 and revealed that it possesses a unique catalytic domain featuring two basic residues in the active site to recognize TPA. Biochemical and mutagenesis studies demonstrated the crucial residues responsible for the substrate specificity of this enzyme.

scholarly journals Phosphorylation of Serine 1106 in the Catalytic Domain of Topoisomerase IIα Regulates Enzymatic Activity and Drug Sensitivity

2003 ◽  
Vol 278 (15) ◽  
pp. 12696-12702 ◽  
Author(s):  
Kenichi Chikamori ◽  
Dale R. Grabowski ◽  
Michael Kinter ◽  
Belinda B. Willard ◽  
Satya Yadav ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Drug Sensitivity ◽  
Catalytic Domain ◽  
Topoisomerase Iiα

scholarly journals Mechanism of Action for HDAC Inhibitors—Insights from Omics Approaches

2019 ◽  
Vol 20 (7) ◽  
pp. 1616 ◽  
Author(s):  
Wenbo Li ◽  
Zheng Sun
Keyword(s):  
Clinical Trials ◽  
Enzymatic Activity ◽  
Histone Deacetylase ◽  
Mechanism Of Action ◽  
Histone Deacetylase Inhibitors ◽  
Catalytic Domain ◽  
Hdac Inhibitors ◽  
Mechanistic Studies ◽  
Low Toxicity ◽  
Strict Specificity

Histone deacetylase inhibitors (HDIs) are a class of prominent epigenetic drugs that are currently being tested in hundreds of clinical trials against a variety of diseases. A few compounds have already been approved for treating lymphoma or myeloma. HDIs bind to the zinc-containing catalytic domain of the histone deacetylase (HDACs) and they repress the deacetylase enzymatic activity. The broad therapeutic effect of HDIs with seemingly low toxicity is somewhat puzzling when considering that most HDIs lack strict specificity toward any individual HDAC and, even if they do, each individual HDAC has diverse functions under different physiology scenarios. Here, we review recent mechanistic studies using omics approaches, including epigenomics, transcriptomics, proteomics, metabolomics, and chemoproteomics, methods. These omics studies provide non-biased insights into the mechanism of action for HDIs.

scholarly journals A trapped human PPM1A–phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity

2018 ◽  
Vol 293 (21) ◽  
pp. 7993-8008 ◽  
Author(s):  
Subrata Debnath ◽  
Dalibor Kosek ◽  
Harichandra D. Tagad ◽  
Stewart R. Durell ◽  
Daniel H. Appella ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Metal Ions ◽  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Catalytic Domain ◽  
Protein Phosphatases ◽  
Random Order ◽  
Structural Features

Metal-dependent protein phosphatases (PPM) are evolutionarily unrelated to other serine/threonine protein phosphatases and are characterized by their requirement for supplementation with millimolar concentrations of Mg2+ or Mn2+ ions for activity in vitro. The crystal structure of human PPM1A (also known as PP2Cα), the first PPM structure determined, displays two tightly bound Mn2+ ions in the active site and a small subdomain, termed the Flap, located adjacent to the active site. Some recent crystal structures of bacterial or plant PPM phosphatases have disclosed two tightly bound metal ions and an additional third metal ion in the active site. Here, the crystal structure of the catalytic domain of human PPM1A, PPM1Acat, complexed with a cyclic phosphopeptide, c(MpSIpYVA), a cyclized variant of the activation loop of p38 MAPK (a physiological substrate of PPM1A), revealed three metal ions in the active site. The PPM1Acat D146E–c(MpSIpYVA) complex confirmed the presence of the anticipated third metal ion in the active site of metazoan PPM phosphatases. Biophysical and computational methods suggested that complex formation results in a slightly more compact solution conformation through reduced conformational flexibility of the Flap subdomain. We also observed that the position of the substrate in the active site allows solvent access to the labile third metal-binding site. Enzyme kinetics of PPM1Acat toward a phosphopeptide substrate supported a random-order, bi-substrate mechanism, with substantial interaction between the bound substrate and the labile metal ion. This work illuminates the structural and thermodynamic basis of an innate mechanism regulating the activity of PPM phosphatases.

THROMBIN PROPERTIES

1957 ◽  
Vol 35 (1) ◽  
pp. 743-758 ◽  
Author(s):  
Edward Ronwin
Keyword(s):  
Ionic Strength ◽  
Substrate Specificity ◽  
Enzymatic Activity ◽  
Enzymatic Properties ◽  
Organic Reagents

The enzymatic properties of thrombin have been examined and compared with those of two related enzymes, plasmin and trypsin. The effects of factors such as pH, substrate specificity, ionic strength, cations, anions, and organic reagents on the enzymatic activity of thrombin have been studied. While the three enzymes discussed possess differences, such similarities as were observed are quite striking and permit their classification into one group as tryptic enzymes.

Functional analysis of two isoforms of phosphatidylethanolamine N-methyltransferase

2010 ◽  
Vol 432 (2) ◽  
pp. 387-398 ◽  
Author(s):  
Shin-ya Morita ◽  
Atsuko Takeuchi ◽  
Shuji Kitagawa
Keyword(s):  
Functional Analysis ◽  
Endoplasmic Reticulum ◽  
Substrate Specificity ◽  
Enzymatic Activity ◽  
The Other ◽  
Human Embryonic Kidney ◽  
Enzymatic Assays ◽  
Hek 293 ◽  
293 Cells ◽  
High Mannose

The enzyme catalysing the conversion of PE (phosphatidylethanolamine) into PC (phosphatidylcholine), PEMT (PE N-methyltransferase), exists as two isoforms, PEMT-L (longer isoform of PEMT) and PEMT-S (shorter isoform of PEMT). In the present study, to compare the functions of the two isoforms of PEMT, we established HEK (human embryonic kidney)-293 cell lines stably expressing PEMT-L and PEMT-S. Both PEMT-L and PEMT-S were localized in the ER (endoplasmic reticulum). PEMT-L, but not PEMT-S, was N-glycosylated with high-mannose oligosaccharides. The enzymatic activity of PEMT-S was much higher than that of PEMT-L. By using novel enzymatic assays for measuring PC and PE, we showed that PEMT-L and PEMT-S expression remarkably increased the cellular PC content, whereas the PE content was decreased by PEMT-S expression, but was hardly affected by PEMT-L expression. The cellular content of phosphatidylserine was also reduced by the expression of PEMT-L or PEMT-S. MS analyses demonstrated that the expression of PEMT-S led to more increases in the molecular species of PC and PC-O (ether-linked PC) with longer polyunsaturated chains than that of PEMT-L, whereas the PC-O species with shorter chains were increased more by PEMT-L expression than by PEMT-S expression, suggesting a difference in the substrate specificity of PEMT-L and PEMT-S. On the other hand, various PE and PE-O species were decreased by PEMT-S expression. In addition, PEMT-L and PEMT-S expression promoted the proliferation of HEK-293 cells. Based upon these findings, we propose a model in which the enzymatic activity and substrate specificity are regulated by the glycosylated N-terminal region of PEMT-L localized in the ER lumen.

scholarly journals Prediction of a common β-propeller catalytic domain for fructosyltransferases of different origin and substrate specificity

2000 ◽  
Vol 9 (11) ◽  
pp. 2285-2291 ◽  
Author(s):  
Tirso Pons ◽  
Lázaro Hernández ◽  
Frank R. Batista ◽  
Glay Chinea
Keyword(s):  
Substrate Specificity ◽  
Catalytic Domain ◽  
Different Origin
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