• However, both the substrate transporting cavity and the determinants of substrate specificity within the cavity of UMAMITs for any substrate remains unknown. (frontiersin.org)
  • Tyr76 participates in hydrogen bonding with the lactone carbonyl which is predicted to aid in substrate specificity. (wikipedia.org)
  • SDR, specificity-determining residue. (plos.org)
  • The NBDs in ABCG2 remain in contact with one another even without a bound substrate, providing greater substrate specificity as the entrance to the transporter is not as globular as other ABC transporters like ABCB1 or ABCC1. (proteopedia.org)
  • Several isozymes of this gene family exist in vertebrates, which vary in cellular location and substrate specificity. (nih.gov)
  • The GlcNac (β1-6) residue is the only anomeric configuration that can effect the specificity of the enzyme enabling cleavage of the non-reducing β1-4 Galactose. (neb.com)
  • We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. (biomedcentral.com)
  • The second factor, termed peptide specificity, describes the interaction between amino acid residues in the catalytic domain of the protein kinase and the substrate residues that surround the phosphorylated residue. (biomedcentral.com)
  • The relative contribution of substrate recruitment and peptide specificity to protein kinase substrate specificity varies between protein kinases. (biomedcentral.com)
  • However, it is recognised that for many protein kinase families, particularly those that phosphorylate Ser/Thr residues, peptide specificity is the major factor that determines substrate specificity. (biomedcentral.com)
  • The prediction of peptide specificity is therefore the basis for most of the available computational methods aimed at predicting substrates of protein kinases. (biomedcentral.com)
  • We are interested in the substrate - enzyme interaction, and especially in the interactions that are likely to direct the specificity of the enzyme. (lu.se)
  • As both enzymes bind biphosphate substrates, each half barrel has a phosphate-binding motif, and HisF even exhibits limited HisA catalytic activity. (the-scientist.com)
  • Site directed mutagenesis was used to check the catalytic role of residue C his 134, which is in a position to interact with the carbonyl group of CP, and was a candidate for bearing a group whose deprotonation is involved in catalytic efficiency. (europa.eu)
  • The results establish that C his 134 is indeed the residue interacting with the carbonyl group of CP but that it is not directly involved in the catalytic mechanism. (europa.eu)
  • Cyclic AMP binds to specific locations on the regulatory units of the protein kinase, and causes dissociation between the regulatory and catalytic subunits, thus enabling those catalytic units to phosphorylate substrate proteins. (wikipedia.org)
  • Glutamine amidotransferase domian (type G) has SH protease-like catalytic residues. (shroomery.org)
  • The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. (biomedcentral.com)
  • Crystal structures of protein kinases with bound substrate peptides show that substrate residues at positions -3 to +3 relative to the phosphorylated serine, threonine or tyrosine residue adopt an extended conformation and bind to a pocket in the catalytic domain of the protein kinase [ 8 ]. (biomedcentral.com)
  • The heptapeptide sequence from -3 to +3 that best binds to the pocket is determined by the physicochemical nature of the residues in the catalytic domain that line the pocket and contact the substrate. (biomedcentral.com)
  • The catalytic efficiency is 400-fold higher with ANGIOTENSIN II as a substrate than with ANGIOTENSIN I. Angiotensin-converting enzyme 2 is also is a functional receptor for the spike glycoprotein (SPIKE PROTEIN, CORONAVIRUS) of the CORONAVIRUSES SARS-COV, SARS-COV2, and HCOV-NL63. (bvsalud.org)
  • Here, the catalytic number (V(max)) of S-COMT was somewhat higher than that of MB-COMT for all four substrates. (lu.se)
  • STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. (nih.gov)
  • The mammalian O-GlcNAc hydrolase (OGA) removes O-GlcNAc from serine and threonine residues on intracellular glycoproteins. (rsc.org)
  • The active subunits catalyze the transfer of phosphate from ATP to specific serine or threonine residues of protein substrates. (wikipedia.org)
  • The post-translational modification of proteins by phosphorylation of serine, threonine or tyrosine residues is a ubiquitous process in cellular regulation. (biomedcentral.com)
  • The biosynthesis of GAG chains is initiated by xylosylation of a serine residue of the core protein, followed by galactosylation by beta 4GalT7. (lu.se)
  • Such cases exist: for example, a mutase such as phosphoglucomutase catalyses the transfer of a phospho group from one position to another, and isomerase is a more general term for an enzyme that catalyses any one-substrate one-product reaction, such as triosephosphate isomerase . (wikipedia.org)
  • When enzymes bind multiple substrates, such as dihydrofolate reductase (shown right), enzyme kinetics can also show the sequence in which these substrates bind and the sequence in which products are released. (wikipedia.org)
  • This rate-determining step may be a chemical reaction or a conformational change of the enzyme or substrates, such as those involved in the release of product(s) from the enzyme. (wikipedia.org)
  • in such cases, it is helpful to determine the enzyme structure with and without bound substrate analogues that do not undergo the enzymatic reaction. (wikipedia.org)
  • Beyond this limit the enzyme is saturated with substrate and the reaction rate ceases to increase. (wikipedia.org)
  • In lysosomal storage disorders, the deficiency of a specific lysosomal enzyme interrupts the normal catabolic pathway, resulting in the cellular accumulation of substrates ordinarily degraded by that enzyme. (medscape.com)
  • The use of tight-binding inhibitors such as entacapone enabled the estimation of actual enzyme concentrations and, thereby, comparison of velocity parameters, substrate selectivity, and regioselectivity of the methylation of both enzyme forms. (lu.se)
  • The K(m) values varied considerably, depending on both substrate and enzyme form. (lu.se)
  • On the basis of the X-ray crystallographic 3D structure, an approach including site-directed and random mutagenesis is taken to determine functional important residues and regions. (lu.se)
  • The biosynthesis can also be initiated by exogenously added beta-D-xylopyranosides with hydrophobic aglycons, which thus can act as acceptor substrates for beta 4GalT7. (lu.se)
  • The purpose of the loop is speculated to activate during substrate appropriation and act as a lid which the catalysis occurs. (wikipedia.org)
  • The structure reveals key active-site residues at the domain interface, including His200, Arg297 and Ser179 that are involved in catalysis and/or ligand binding and are highly conserved in TyrA proteins from all three kingdoms of life. (rcsb.org)
  • This conformational change brings the substrate, cofactor and active-site residues into close proximity for catalysis. (rcsb.org)
  • Two major factors determine the formation of a protein kinase-substrate complex [ 4 ]. (biomedcentral.com)
  • The first, termed substrate recruitment, encompasses any process that increases the effective concentration of the protein kinase substrate. (biomedcentral.com)
  • Further, the C215A mutant is capable of removing O-GlcNDAz from a peptide substrate. (rsc.org)
  • Factors that might affect the linearity and dynamic range for detection of BoNT cleavage products were initially examined, including the amount of peptide substrate and internal standard, the timing of cleavage reaction, and the components in the reaction solution. (cdc.gov)
  • Each serotype of BoNT hydrolyzes their protein substrates at different peptide bonds. (cdc.gov)
  • Enzymatic cleavage assays represent an attractive approach where the functional active toxins are detected by monitoring the cleavage of their target substrates, or peptide mimics in most cases, by means of different techniques, such as immunological detection 18 , 19 , capillary electrophoresis 20 , fluorescence analysis 21 , Forster resonance energy transfer (ALISSA) 22 , and high performance liquid chromatography 23 . (cdc.gov)
  • These studies provide a molecular understanding of how MATH-BTB proteins recruit substrates to Cul3 and how their dimerization and conformational variability may facilitate avid interactions with diverse substrates. (rcsb.org)
  • in order to recruit substrates for transport. (proteopedia.org)
  • Within the barrel, it is mainly hydrophobic forces that interact with the substrate. (wikipedia.org)
  • Within the cleft, at least five different subsites interact with the substrate, each subsite binding one monomeric unit of the polysaccharide. (lu.se)
  • To study the role of hydrophobic residues in these reactions, we have mutated three active-site phenylalanines. (hanze.nl)
  • Cavity 2 contains a less hydrophobic environment and, as a result, substrates are released due to hydrophobic mismatch. (proteopedia.org)
  • Here, we set out to identify amino acid residues responsible for glucosinolate transport activity of the main seed glucosinolate exporter UMAMIT29 in Arabidopsis thaliana . (frontiersin.org)
  • Transport activity assays of mutant variants with a single point amino acid substitution in each site UMAMIT29 suggest that five of these residues are critical for glucosinolate transport. (frontiersin.org)
  • We invoke various groups as potential proton acceptors-namely, the phosphate and leucyl amino groups of leucyl-adenylate, the A76 base of tRNA, and the Asp80 and Glu532 residues of the protein-and consider both metal-assisted and metal-free reactions. (nih.gov)
  • Mutation of alphaF146, betaF24 and betaF57 to Tyr, Trp, Ala or Leu yielded mutants that were still capable of hydrolysing the chromogenic substrate 2-nitro-5-[(phenylacetyl)amino]-benzoic acid. (hanze.nl)
  • and even the role of particular amino acid residues in the mechanism. (wikipedia.org)
  • Two recently published human COMT cDNA sequences differed in the position of S-COMT amino acid 108, the residue being either Val-108 [Lundstrom et al. (lu.se)
  • A comparison of the putative substrate binding site of homologs within the brassicaceous-specific, glucosinolate-transporting clade with the non-brassicaceous-specific, non-glucosinolate-transporting UMAMIT32 clade identified 11 differentially conserved sites. (frontiersin.org)
  • Based on our model, we proposed a substrate-transporting cavity of UMAMIT29 defined by helix I to IV and VI-IX and selected 51 residues as putative substrate binding sites based on solvent accessibility ( Figure 1 ). (frontiersin.org)
  • Predikin now consists of two components: (i) PredikinDB, a database of phosphorylation sites that links substrates to kinase sequences and (ii) a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining residues, generate scoring matrices and score putative phosphorylation sites in query sequences. (biomedcentral.com)
  • New features in Predikin include the use of SQL queries to PredikinDB to generate predictions, scoring of predictions, more reliable identification of substrate-determining residues and putative phosphorylation sites, extended options to handle protein kinase and substrate data and an improved web interface. (biomedcentral.com)
  • Structural flexibility between the substrate-binding MATH and Cul3-binding BTB/3-box domains potentially allows a SPOP dimer to engage multiple SBCs found within a single substrate, such as Puc. (rcsb.org)
  • An example of enzymes that bind a single substrate and release multiple products are proteases , which cleave one protein substrate into two polypeptide products. (wikipedia.org)
  • Protein kinases and their substrates regulate essentially all cellular processes through complex regulatory networks, in which phosphorylated proteins act as switches that tune the response of the cell to environmental stimuli. (biomedcentral.com)
  • Xylose appears to be the optimal acceptor substrate for galactosylation by beta 4GalT7. (lu.se)
  • After substrates bind in Cavity 1, ATP binds each NBD leading to the transporter shifting from inward-facing to outward-facing. (proteopedia.org)
  • Dihydrofolate reductase from E. coli with its two substrates dihydrofolate (right) and NADPH (left), bound in the active site. (wikipedia.org)
  • An ionic network consisting of Arg297 (a key residue for tyrosine binding), a water molecule, Asp206 (from the loop between β5 and β6) and Arg365' (from the additional C-terminal helix of the adjacent monomer) is observed that might be involved in gating the active site. (rcsb.org)
  • When the corresponding Glu NH2 residue of Escherichia coli anabolic OTCase was exchanged for Glu, no cooperativity resulted, however. (europa.eu)
  • Mutation of one of these residues, C215, results in mutant enzymes that are able to hydrolytically remove O-GlcNDAz from a model compound. (rsc.org)
  • Due to the hydrophobicity of the substrate and product of AbyU, organic solvents are required to aid in dissolution and to prevent aggregation. (wikipedia.org)
  • However, at the same time vegetable crop residues are a vital link in closing the nutrient and organic matter cycle of soils. (mdpi.com)
  • Humic substrates are organic soil amendment that is often used for enhancing chemical and biochemical properties in soil. (deepdyve.com)
  • The residue remained at the end of this process was further vermicomposted to prepare organic amendment having total nitrogen content 1.34 ± 0.07 mg g−1 with C/N ratio 10.87 ± 0.92. (deepdyve.com)
  • In close cooperation with the Entsorgungsverband Saar (EVS - Association for disposal in the Federal State of Saarland, Germany) and the Ministerium für Umwelt, Energie und Verkehr des Saarlandes (MUEV - Federal State Ministry for environment, energy and traffic of Saarland, Germany) the IZES gGmbH is developing three regional strategies for the utilisation of organic residues. (izes.de)
  • This study demonstrates that almond processing residues recycled into the soil as biosolarization substrates produce a high diversity of bioactive degradation compounds on a field scale, with low potential of non-target risks to humans.Implications: This manuscript has implications for two policy goals in the state of California: to reduce landfill disposal of organic waste, and to reduce emissions from soil fumigants. (cdc.gov)
  • When used in conjunction with α1-2,3 Mannosidase, the α1-6 Mannosidase will cleave α1-6 Mannose residues from branched carbohydrate substrates. (neb.com)
  • In sialidosis, the deficiency of lysosomal alpha- N -acetyl neuraminidase prevents the normal degradation of glycoproteins containing sialic acid residues. (medscape.com)
  • 1975. The effect of atmospheric levels of pesticides on pesticide residues in rabbit adipose tissue and blood sera. (cdc.gov)
  • with residues from each subunit in Cavity 1. (proteopedia.org)
  • A site on the alpha subunit acts against negatively charged sulfated substrates, while a site on the beta subunit acts against neutral water-soluble substrates. (medscape.com)
  • for example, glyceraldehyde 3-phosphate dehydrogenase has three substrates and two products. (wikipedia.org)
  • In this study, a novel technique was developed for extracting humic substrates by recycling factory tea waste and potential of those extracted humic substrates for improving soil properties and tea productivity was evaluated under field condition. (deepdyve.com)
  • Under field condition, extracted humic substrates lead up to 6% increase in tea productivity and improved soil chemical properties. (deepdyve.com)
  • Different almond variety residues produced distinct volatile profiles, and nonpareil-amended soils had a much richer and more diverse profile, as well as a fivefold greater VOC abundance, than pollinator-amended soil. (cdc.gov)
  • Here, recycling almond residues as soil amendments promoted the rapid formation of VOCs which may act as alternatives to chemical fumigants. (cdc.gov)
  • In the largest E3 ligase subfamily, Cul3 binds a BTB domain, and an associated protein-interaction domain such as MATH recruits substrates for ubiquitination. (rcsb.org)
  • The kinases are represented in complex with an ATP molecule (green, orange, blue, red) and a substrate-mimicking inhibitor (PKIA, yellow). (plos.org)
  • One molecule of ATP is hydrolyzed to transport substrates across the cell membrane while the second molecule of ATP is hydrolyzed to reset the transporter to its inward-facing conformation. (proteopedia.org)
  • Using homology modeling, we identified OGA residues proximal to the N -acyl position of O-GlcNAc substrate. (rsc.org)
  • It hydrolyzes terminal, non-reducing beta-D-galactose residues in beta-D-galactosides. (novusbio.com)
  • Based on a predicted model of UMAMIT29, we propose that the substrate transporting cavity consists of 51 residues, of which four are highly conserved residues across all the analyzed homologs of UMAMIT29. (frontiersin.org)
  • Based on distance-based protein folding tools, we predict the substrate-transporting cavity of UMAMIT29. (frontiersin.org)
  • We hypothesised that the transport cavity contains highly conserved residues that are key for the transport activity. (frontiersin.org)
  • The protein is in the inward-facing conformation with Cavity 1 open to the cytosol for substrate recruitment, the Leucine Plug intact, and Cavity 2 completely occluded. (proteopedia.org)
  • This collapse forces the substrate to move forward to Cavity 2 as there is no longer room in Cavity 1 to accommodate substrates. (proteopedia.org)
  • To test this, we aligned 97 protein sequences consisting of homologs of UMAMIT clade I from 27 plant species and created sequence logos containing the 51 residues identified in the structural analysis ( Supplementary Figure 1 ). (frontiersin.org)
  • Here, we combine in-vitro structural measurements, which used EPR spectroscopy and UV-Vis measurements, with cell experiments to explore the role of the various methionine residues in CusB. (biorxiv.org)
  • This example assumes the simplest case of a reaction with one substrate and one product. (wikipedia.org)
  • By combining the results from two-stage quantification, 4 or 5 orders of magnitude in dynamic range were achieved for the detection of the serotypes of BoNT/A, /B, /E, or /F. The effect of multiplexing the assay by mixing substrates for different BoNT serotypes into a single reaction was also investigated in order to reduce the numbers of the cleavage reactions and to save valuable clinical samples. (cdc.gov)
  • To do this, we designed and synthesized the fluorescently labelled substrate Mca-AVLQ↓SGFRK(Dnp)K, derived from the N-terminal autocleavage sequence of the viral protease, for time-dependent kinetic analysis (Extended Data Fig. 1e ). (nature.com)
  • Reactions with three or four substrates or products are less common, but they exist. (wikipedia.org)
  • Reactions were incubated at 37°C. The substrate depicted in (E) will not cut to completion. (neb.com)
  • Deficient activity of these enzymes leads to accumulation of the substrate inside neuronal lysosomes, leading to cell death. (medscape.com)
  • By comparing differentially conserved residues within the predicted cavities between glucosinolate-transporting and non-glucosinolate-transporting UMAMITs, we identify 11 candidate residues. (frontiersin.org)
  • Substrates are transported through ABCG2 via two cavities separated by a leucine plug (Figure 2). (proteopedia.org)
  • The SPS-TM-A test specimen is manufactured on a glassy carbon substrate with a size of 8 x 8mm with various sizes of synthetic particles containing Pb, Sb and Ba. (tedpella.com)
  • It is recommended that the BSE signal of the SEM is used for imaging the particles since this a high contrast signal difference between the Pb/Ba/Sb particles and the glassy carbon substrate. (tedpella.com)
  • On harder surfaces, the mechanism of action is primarily the ablation where the focused beam of laser dislodges microscopic particles from the substrate. (wikipedia.org)
  • This isozyme is the most abundant, is ubiquitously expressed and localized in the cytoplasm, and whose preferred substrate is hydrogen peroxide. (nih.gov)
  • Others join two substrates together, such as DNA polymerase linking a nucleotide to DNA . (wikipedia.org)
  • It cleaves a single C-terminal residue from a distinct range of substrates. (bvsalud.org)
  • If this structure exists in any substrate it will be impervious to cleavage by α1-6 Mannosidase. (neb.com)
  • The objective of this work was to optimize the production and characterize α-amylase produced by Aspergillus niger through solid state fermentation, using leaf residues of C. linearifolius as substrate. (researchain.net)
  • Different solid substrates like banana pseudo-stem and leaf vein are rich in starch. (researchgate.net)
  • More knowledge of the underlying mechanism is needed to attain a full understanding of CusB functioning, which is associated with targeting specific and crucial residues in CusB. (biorxiv.org)
  • The purpose of this study was to (1) profile volatiles that may contribute to pest control under field conditions and (2) measure volatile compounds that may present nuisance or exposure risks for humans near biosolarized fields where larger-scale anaerobic degradation of residues occurs. (cdc.gov)
  • Therefore, the results demonstrate that the residues of C. linearifolius can be used as a substrate for A. niger in the production of enzymatic extracts, such as α-amylase. (researchain.net)
  • Ensure that you have run qmmmpbsa-ptch for the substrate and product states, and that the results are in the Ptch subdirectories. (lu.se)
  • When each of the 11 residues of UMAMIT29 was individually mutated into the corresponding residue in UMAMIT32, five mutant variants (UMAMIT29#V27F, UMAMIT29#M86V, UMAMIT29#L109V, UMAMIT29#Q263S, and UMAMIT29#T267Y) reduced glucosinolate transport activity over 75% compared to wild-type UMAMIT29. (frontiersin.org)
  • This suggests that these residues are key for UMAMIT29-mediated glucosinolate transport activity and thus potential targets for blocking the transport of glucosinolates to the seeds. (frontiersin.org)
  • THe OTCase lost most of its homotropic cooperativity and gained anabolic activity when residue glutamic acid (Glu) 106, near the CP binding site, was replaced by alanine (Ala) or glycine (Gly). (europa.eu)
  • among them we have to mention the water contamination due to the residues inherent to the activity. (scirp.org)
  • There has also been an increase in the amount of residues and substrates produced with the intensification of the mining activity. (scirp.org)