• The N-terminus domain includes the catalytically active portion of the enzyme, while the C-terminus domain has a specificity for binding to ulvan, making it the substrate-binding domain. (wikipedia.org)
  • The C116H mutant acquired a novel β-elimination activity and lead a drastic conformation change in the histidine residue at position 116 by binding the substrate, suggesting that this His residue affects the reaction specificity of C116H. (elsevierpure.com)
  • Furthermore, we suggest that Lys240 * is important for substrate recognition and structural stability and that Asp241 * is also involved in substrate specificity in the elimination reaction. (elsevierpure.com)
  • Based on this, we suggest that the hydrogen-bond network among Cys116, Lys240 * , and Asp241 * contributes to substrate specificity that is, to L-methionine recognition at the active site in MGL-Pp. (elsevierpure.com)
  • The regulatory subunits of PP2A holoenzyme determine the substrate specificity. (eu.org)
  • Activity assays and molecular dynamics studies of the resultant variants showed that the substrate specificity of Ec MAL was modified by adjusting the polarity of the binding pocket and the degree of flexibility of the entrance tunnel. (springeropen.com)
  • Among ALs, MAL has attracted much attention because of its broad substrate specificity and its acceptance of a variety of amines (Leese et al. (springeropen.com)
  • Substrate specificities == The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. (cazypedia.org)
  • To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exolyase). (ox.ac.uk)
  • Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirms that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform that can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. (ox.ac.uk)
  • Complete pectin catabolism requires synergy between multiple pectinases with different substrate specificities (Kamijo et al. (springeropen.com)
  • Family 22 Polysaccharide Lyases (PL22s) contain two subfamilies and several outlier sequences [ 1 ]. (cazypedia.org)
  • compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. (cazypedia.org)
  • A lyase is a class of enzyme that catalyzes the breakdown of chemical bonds through an elimination reaction mechanism, rather than a substitution reaction mechanism (hydrolysis and oxidation). (wikipedia.org)
  • Mass spectrometry sequencing followed by polymerase chain reaction amplification determined that a complete ulvan lyase gene contains ≈1536 base pairs and ≈512 amino acids (after translation). (wikipedia.org)
  • We attempt to elucidate the mechanism by which the enzyme facilitates this reaction through interactions between active-site residues and the substrate. (edu.au)
  • We propose a detailed model for the catalytic reaction mechanism of HMG-CoA lyase based on the examination of previously reported product complexes of other DRE-TIM metallolyases and induced fit substrate docking studies conducted using the crystal structure of human HMG-CoA lyase (reported in the accompanying paper by Fu, et al. (rcsb.org)
  • This paper focusing on the difference in the α-glucosidase families reviews the structural information including the catalytic amino acid residues of nucleophile and acid/base catalyst, the recognition of substrate molecule, and the intermediate in the transition state of hydrolytic reaction. (go.jp)
  • In other words, the substrate and product of the reaction are isomers . (cliffsnotes.com)
  • At the end of the reaction, equilibrium is reached, no net conversion of substrate to product occurs, and either curve approaches the horizontal. (cliffsnotes.com)
  • Just as any other chemical reaction can be favored by increasing the concentration of a reactant, the formation of an enzyme‐substrate complex can be favored by a higher concentration of substrate. (cliffsnotes.com)
  • The enzyme acts on the product of the reaction catalysed by EC 1.14.17.3 peptidylglycine monooxygenase, thus removing a terminal glycine residue and leaving a des-glycine peptide amide. (genome.jp)
  • Structural modeling of complexes with the flavin, coenzyme, and substrate suggested specific residues contributing to the NbaA catalytic activity, assuming a ping-pong reaction mechanism. (canada.ca)
  • This in turn would render the molecule an inhibitor as desired high compound concentration for high reaction turnover would compete with the originally intended substrate. (ki.se)
  • In June 2022, we were first to report cellularly active organocatalysts - OGG1 organocatalytic switches assist the enzyme in reaction turnover and diversification of substrate and product scope. (ki.se)
  • The generated reaction product releases the Lys249 residue and OGG1 can enter a new catalytic cycle. (ki.se)
  • The first coupled assay uses a human bone phosphatase, PHOSPHOl, which is highly specific for the PE product of the lyase reaction. (ed.ac.uk)
  • ALs, belonging to the enolase family, specifically use unsaturated carboxylates as substrates for the hydroamination reaction to generate unnatural amino acids and their derivatives (Turner 2011 ). (springeropen.com)
  • Galactose oxidase is an extracellular monomeric enzyme which catalyzes the stereospecific oxidation of a broad range of primary alcohol substrates and possesses a unique mononuclear copper site essential for catalyzing a two-electron transfer reaction during the oxidation of primary alcohols to corresponding aldehydes. (unl.edu)
  • The second redox active center necessary for the reaction was found to be situated at a tyrosine residue. (unl.edu)
  • The specific catalytic residues found in this region are Arg117, Gln160, Tyr281, and Lys162. (wikipedia.org)
  • The crystal structure of cystathionine gamma-lyase (CGL) from yeast has been solved by molecular replacement at a resolution of 2.6 A. The molecule consists of 393 amino acid residues and one PLP moiety and is arranged in the crystal as a tetramer with D2 symmetry as in other related enzymes of the Cys-Met-metabolism PLP-dependent family like cystathionine beta-lyase (CBL). (unipr.it)
  • The C-terminal part contains a ~170 residues regulatory domain, termed Effector binding Domain (ED) as it may bind a small effector or signal molecule. (expasy.org)
  • The molecule can replace the excised base and interact with the same amino acid residues. (ki.se)
  • However, this interpretation ignores enzymes with complex biochemistry, where substrate hydrolysis is achieved by consecutive steps of replacement and cleavage. (ki.se)
  • ATP citrate-lyase (EC 2.3.3.8 ) [ 1 ], the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues, catalyzes the formation of acetyl-CoA and oxaloacetate from citrate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. (expasy.org)
  • Succinyl-CoA ligase (GDP-forming) (EC 6.2.1.4 ) [ 2 ] is a mitochondrial enzyme that catalyzes the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. (expasy.org)
  • Since Tsc13 is an essential enzyme, a combination of homology modelling and site-saturation mutagenesis was used to identify residues that would impair its activity towards p-coumaroyl-CoA without compromising cell growth. (ruc.dk)
  • This step in the enzyme's mechanism was probed via the mutagenesis of potential residues involved to give insight into this key stage in catalysis whereby the PLP-S1P intermediate is deprotonated releasing the 2E-HEX product. (ed.ac.uk)
  • A combined mutagenesis strategy was used to simultaneously redesign the key residues of the entrance tunnel and binding pocket to explore the possibility of accepting bulky substrates with potential application to chiral drug synthesis. (springeropen.com)
  • In this study, we selected BacPelA, the pectin lyase with the highest expression activity from Bacillus clausii , modified and expressed in Escherichia coli BL21(DE3). (springeropen.com)
  • The optimum pH and temperature of the modified pectin lyase (PGLA-rep4) were 11.0 and 70 °C, respectively. (springeropen.com)
  • After approximately 20 ns of molecular dynamics simulation, the structure of the pectin lyase PGLA-rep4 tended to be stable. (springeropen.com)
  • The aim of this study was to investigate the effects of enzymatic treatments (pectinase, pectin lyase, and cellulase) on the in vitro digestion and fermentation characteristics of whole mulberry fruit juice. (uneatlantico.es)
  • displays the lowest reported pH optimum for a pectate lyase (7.3 - 7.7) [ 3 ], which is substantially lower than other families that deploy catalytic arginines or lysines in the β-elimination of pectate. (cazypedia.org)
  • Alkaline pectate lyase has developmental prospects in the textile, pulp, paper, and food industries. (springeropen.com)
  • In CBLs this position is occupied by either tyrosine or hydrophobic residues directing binding of CTT such that S is in the in gamma-position. (unipr.it)
  • The pocket is essentially linear, with a basic patch interacting with the acidic residues in the C-terminal end of the motif and the hydrophobic patch interacting with the two key hydrophobic residues of the motif. (eu.org)
  • Four different enzymes share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. (expasy.org)
  • The second pattern, which is located some 50 residues to the C-terminal of the first one, includes the active site phosphorylated histidine residue. (expasy.org)
  • Here we present crystal structures of the HMG-CoA lyases from Bacillus subtilis and Brucella melitensis at 2.7 and 2.3 A resolution, respectively. (rcsb.org)
  • Recently, it was reported that the dehydration process in thioviridamide relies on a distinct dehydratase complex which showcases the activities of a phosphotransferase TvaC for serine/threonine phosphorylation and a lyase TvaD for subsequent phosphate elimination. (authorea.com)
  • Plant CGSs use homoserine phosphate instead of O-succinyl-homoserine as one substrate. (unipr.it)
  • Although the enzyme has the anticipated triose-phosphate isomerase (TIM) barrel fold, the catalytic center contains a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel, contrary to the predictions of homology models. (rcsb.org)
  • Other transferases move phosphate groups between ATP and other compounds, sugar residues to form disaccharides, and so on. (cliffsnotes.com)
  • Identification and characterisation of novel sphingosine-1-phosphate lyases in Burkholderia ssp. (ed.ac.uk)
  • The irreversible breakdown of SIP is catalysed by sphingosine-1-phosphate lyase (SIPL), a pyridoxal 5'-phosphate (PLP) dependent enzyme that catalyses the retro-aldol-like cleavage of SIP to (2E)-hexadecenal (2E-HEX) and phosphoethanolamine (PE). (ed.ac.uk)
  • Ab initio molecular orbital calculations are used to examine the mechanism of action of B12-dependent ethanolamine ammonia-lyase involving the conversion of 2-aminoethanol to acetaldehyde plus ammonia. (edu.au)
  • The functional groups transferred by these lyase enzymes include amino groups, water, and ammonia. (cliffsnotes.com)
  • The polysaccharide lyase family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. (ox.ac.uk)
  • From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel β-helix fold shared by all these enzymes, the substrate-binding site harbors the same overall conserved structures and organization. (ox.ac.uk)
  • A structural similarity search making use of the crystal structure of Cip1 generated two hits with high scores and published structures, a glucuronan lyase from H. jecorina (PDB ID: 2ZZJ) and an alginate lyase in the Chlorella virus (PDBID: 3GNE). (ezh2inhibitor.com)
  • PAM substrates generated by expressing peptidylglycine substrates (glucagon-like peptide 1-Gly, peptide YY-Gly and neuromedin U-Gly) fused to the C-terminus of immunoglobulin Fc in CHO cell lines producing targeted PAM. (biomedcentral.com)
  • PAM contains two catalytic domains, peptidylglycine α-hydroxylating monooxygenase (PHM) and peptidyl-α-hydroxyglycine α-amidating lyase (PAL). (biomedcentral.com)
  • The enzymes act sequentially, first converting the peptidylglycine substrate into a short-lived peptidyl-α-hydroxyglycine intermediate and then cleaving the C-N bond to produce the amidated peptide and glyoxylate [ 2 ]. (biomedcentral.com)
  • however, whether this protein is a lyase has yet to be determined. (cazypedia.org)
  • The fluorescence of the single tryptophan residue at position 59 in apocytochrome c , the biosynthetic precursor of the inner mitochondrial membrane protein cytochrome c , was studied in small unilamellar vesicles composed of phosphatidylserine (PS) and phosphatidylcholine (PC) with or without specifically Br-labelled acyl chains at the sn -2 position. (ornine.best)
  • The 534 amino acid residues contained in the ribosomal protein are reduced to 486 by cleavage at the N -terminus upon import to the mitochondrion. (medscape.com)
  • The more substrate is present, the greater the initial velocity, because enzymes act to bind to their substrates. (cliffsnotes.com)
  • Based on substrates and mechanism of action, pectinase is classified into the following sub-types: protopectinase, pectinesterase, and depolymerase (Kashyap et al. (springeropen.com)
  • NDKs from bacterial and other systems contain the conserved HGSD motif, where the His residue is required for the biochemical activities, namely the NTPase (AT-Pase and GTPase), NTP synthesising, and autophosphorylation activities of the enzyme. (openbiochemistryjournal.com)
  • These observations demonstrate that the H117 residue in the HGSD motif is required for the biochemical activities of MsmNDK. (openbiochemistryjournal.com)
  • Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. (cazypedia.org)
  • Although OGG1 is no significant AP-lyase in cells, DNA glycosylases with pronounced β- or β,δ-AP lyase activity exist in humans and other species. (ki.se)
  • Half of the sequenced peptides from an ulvan lyase gene (30 kDa) were isolated in the N-terminus of the peptide, with an average length of 25 amino acids. (wikipedia.org)
  • These results are puzzling, since peptides terminating with -Phe-Gly are far better substrates for PAM that peptides terminating with -Pro-Gly, using test tube assays and purified enzyme [ 1 ]. (biomedcentral.com)
  • 1YDN: Crystal Structure of the HMG-CoA Lyase from Brucella melitensis, Northeast Structural Genomics Target LR35. (rcsb.org)
  • Based on structural interrogation of the enzyme, candidate residues are proposed as the possible base in the Burkholderia isoforms of the enzyme. (ed.ac.uk)
  • Cys116, Lys240 * , and Asp241 * (asterisks indicate residues from the second subunit of the active dimer) at the active site of L-methionine γ-lyase of Pseudomonas putida (MGL-Pp) are highly conserved among heterologous MGLs. (elsevierpure.com)
  • Additional synergistic interactions between the spectator hydroxyl group in the substrate and active-site residues on the enzyme are required to lower the barrier height to a value consistent with experimental observations. (edu.au)
  • In CGL and CBL the pseudosymmetric substrate must dock at the active site in different orientations, with S in gamma-position (CBL) or in delta-position (CGL). (unipr.it)
  • The active site of PHM contains two copper residues, each of which is essential for activity. (biomedcentral.com)
  • PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. (embl.de)
  • Libraries of residues capable of lining the active center of Ec MAL were then constructed and screened by an effective activity solid-phase color screening method using tyrosinase as a cascade catalyst system. (springeropen.com)
  • Ulvan lyase degrades ulvan by catalyzing the endolytic cleavage of the glycosidic linkages in glycosides. (wikipedia.org)
  • Surprisingly, the residues forming this cation-binding site and most of their interaction partners are shared with three other TIM barrel enzymes that catalyze diverse carbon-carbon bond cleavage reactions believed to proceed through enolate intermediates (4-hydroxy-2-ketovalerate aldolase, 2-isopropylmalate synthase, and transcarboxylase 5S). (rcsb.org)
  • L..[IVLWC].E). One of, but not both, the amino acids in position P1 or P4 of the motif can be a variable hydrophobic residue for B56 binding, while P6 has the invariant glutamic acid. (eu.org)
  • Most iclR-type transcription regulators are repressors of specific catabolic genes in the absence of specific substrates, while excess of a specific effector triggers de-repression. (expasy.org)
  • Degradation kinetics models and chemical composition data of LMCS showed the GlcA residues of chondroitin-4-sulfate (CSA) may be preferentially attacked. (bvsalud.org)
  • Dehydration of serine/threonine residues necessitates the activity of a dehydratase enzyme (domain) during the biosynthesis of ribosomally synthesized and post-translationally modified peptide (RiPP). (authorea.com)
  • Remarkably, this dehydratase complex exhibits flexible enzymatic activity and tolerates significant variations in its substrate peptide sequence. (authorea.com)
  • The lyase is highly specific toward α-1, 4-glucosidic bonds and shows negligible activity toward α-1, 6-glucosidic bonds. (go.jp)
  • The enzyme activity of PGLA-rep4, measured at 235 nm with 0.2% apple pectin as the substrate, was 554.0 U/mL, and the specific enzyme activity after purification using a nickel column was 822.9 U/mg. (springeropen.com)
  • Components of those structures show powerful resemblance to Cip1, indicating that Cip1 may have lyase activity. (ezh2inhibitor.com)
  • Though no important lyase activity was identified with the tested carbohydrate supply, we're now a couple of measures closer to being aware of the accurate part of Cip1 in the biomass degradation performed by H. jecorina. (ezh2inhibitor.com)
  • Acetate and propionate production were the highest when faecal bacteria fermented COS-rich solution compared with standard substrates. (bvsalud.org)
  • The 181-amino-acid sequence of NbaB is 35% identical to the 4-hydroxylaminobenzoate lyases (PnbBs) of various 4-nitrobenzoate-assimilating bacteria, e.g. (canada.ca)
  • Our calculations suggest a preferred pathway involving a 1,2-shift in the associated radical and also suggest that interactions between the enzyme and the migrating group of the substrate that afford an almost fully protonated migrating group will lead to the most efficient catalysis. (edu.au)
  • Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. (cazypedia.org)
  • Because if the substrate concentration gets high enough, the enzyme spends all its time carrying out catalysis and no time waiting to bind substrate. (cliffsnotes.com)
  • We also report the determination of the x-ray structure of S1PL2021, with the PLP cofactor bound, at 2.0A resolution which provides an insight into residues potentially involved in catalysis. (ed.ac.uk)
  • A higher degree of flexibility is observed in the intervening and surrounding positions and a stronger binding affinity is observed when the residues at the position P2 or P7-P9 were either phosphorylated or an acidic residue is already present, as the negative charge engages with the basic patch of B56 ( Wang,2016 ). (eu.org)
  • Without ulvan lyase, marine algae like Ulvales would not be able to catalyze the breakdown of ulvan into monosaccharides, a prerequisite for the conversion of carbohydrates to energy through the central sugar metabolism. (wikipedia.org)
  • Throughout the process of in vitro digestion, there was a gradual increase in the percentage of solubilized carbohydrates from the mulberry juice substrate. (uneatlantico.es)
  • 3-Hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) lyase deficiency is a rare inborn error of metabolism characterized by recurrent metabolic crises caused by fasting, intercurrent illness and excessive physical exercise. (biomedcentral.com)
  • S1PL is a PLP Fold type I carbon-carbon bond lyase belonging to the Group II PLP-dependent decarboxylase subfamily and is the terminal enzyme in sphingolipid metabolism. (ed.ac.uk)
  • In methionine gamma-lyase a hydrophic patch operates as recognition site for the methyl group of the methionine substrate. (unipr.it)
  • α-Glucosidase contributing starch and glycogen metabolisms in plant and animal tissue is characterized by the variety in substrate recognition. (go.jp)
  • Both CGLs and bacterial CGSs exhibit gamma-synthase and gamma-lyase activities depending on their position in the metabolic pathway and the available substrates. (unipr.it)
  • Patient with HMG-CoA lyase deficiency whom after diagnosis at 2 years of age was re-admitted 12 years later, after severe metabolic decompensation following consumption of alcohol. (biomedcentral.com)
  • The enzyme 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) lyase catalyzes the terminal steps in ketone body generation and leucine degradation. (rcsb.org)
  • Ulvan lyase belongs to the polysaccharide lyase family, a type of enzyme that primarily functions to cleave glycosidic linkages in polysaccharides. (wikipedia.org)
  • This family represents the N-terminus (approximately 300 residues) of a number of plant and fungal glyoxal oxidase enzymes. (unl.edu)
  • For example, ulvan lyase shares an EC number with other lyase-catalyzed reactions (that act on polysaccharides) that occur in organisms unrelated to Ulvales. (wikipedia.org)
  • Remember that in redox reactions, one substrate is oxidized and one is reduced. (cliffsnotes.com)
  • The second assay employs a recombinant form of human fatty aldehyde dehydrogenase (FALDH) which uses the 2E-HEX as a substrate. (ed.ac.uk)