Structural substrate lyases. Medical search. Frequent questions

The regulatory subunits of PP2A holoenzyme determine the substrate specificity. (eu.org)
Activity is regulated on two levels: overall activity and substrate specificity (as only one RNR catalyses the reduction of all four ribonucleotides under given physiological conditions). (lu.se)
dNTP products regulate the enzyme's specificity for the NTP or NDP substrates. (lu.se)
We have been able to explain how conformational changes a loop spanning the dimer interface communicate the substrate specificity signal to the active site for the class II RNR. (lu.se)
The extensive structural comparison with fold-type I enzymes with known amino acid racemization activities, including the α-amino-ε-caprolactam racemase from Achromobacter obae and the cystathionine β-lyase from Escherichia coli, allows us to identify the active site residues responsible for its nonpolar amino acid recognition and reactivity specificity. (unipr.it)

Proteins containing these repeats most often are enzymes with polysaccharide substrates. (embl.de)
This dissertation explores aspects of the chemistry and evolution of a small class of enzymes catalysing geometrical and structural rearrangements between isomers, the isomerases (EC 5). (researchgate.net)
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)
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)
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)
Nevertheless, from the structural and evolutionary points of view, these proteins may form with the enzymes common to the α-amylase protein family. (go.jp)
The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases [LigD (PDB IDs 4Y98 4Y9D ), LigO (PDB IDs 4YA6 4YAC ), and LigL (PDB IDs 4YAE 4YAG 4YAI )] and the glutathione-dependent lyase LigG (PDB IDs 4YAP 4YAV ) provide new insights into the early and late enzymes in the β-ether degradation pathway. (jbei.org)
Information on substrate flow and regulation through the branch point between flavonol and anthocyanin synthesis is however not fully eluci dated, and for tomato the enzymes acting in the branch point have not been extensively characterised. (chk1inhibitor.com)
Metal centers constitute the active sites of at least one third of all enzymes and determining the assembly mechanism of metallocenters and the electronic and structural properties of metal centers that confer selective and specific catalytic activity present fascinating challenges to inorganic chemists. (uga.edu)
From structural modelling to the genetic modification of enzymes, Capacités offers tailor-made services: screening enzyme strains, developing and refining new enzymes and producing functional and modified enzymes. (capacites.fr)
The structure of rhamnogalacturonase (RGase A) from Aspergillus aculeatus [ 4 ] revealed the signature parallel β-helix architecture common to several pectin active enzymes including family 1 pectate lyases ( PL1 ). (cazypedia.org)
The GH28 enzymes are distinguished from the lyases by having four, not three, parallel β-sheets extending along their longitudinal axes. (cazypedia.org)

We have examined the activities of different preparations of heparin and heparan sulfate lyases from Flavobacterium heparinum. (rpi.edu)

The tertiary structures of pectate lyases and rhamnogalacturonase A show a stack of parallel beta strands that are coiled into a large helix. (embl.de)
Three bacterial pectate lyases, a pectin lyase from Aspergillus niger, thestructures of rhamnogalacturonase A from Aspergillus aculeatus, RGase A,and the P22-phage tailspike protein, TSP, display the right-handedparallel beta-helix architecture first seen in pectate lyase. (embl.de)
compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. (cazypedia.org)
which despite belonging to [[PL1]], have diverged significantly from the pectate lyases. (cazypedia.org)

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)

Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity. (ox.ac.uk)
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)

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 study of the evolution of proteins has been traditionally undertaken from a sequence and structural point of view. (researchgate.net)
These superhelical structures present an extensive solvent-accessible surface that is well suited to binding large substrates such as proteins and nucleic acids. (eu.org)
Additionally, the structure of DS-epi1 reveals a high structural similarity to proteins from several families of bacterial polysaccharide lyases. (scilifelab.se)
Access structural information, both raw diffraction data and PDB entries, for proteins that could be optimized to improve the production of advanced biofuels and bioproducts. (jbei.org)
Interactions of heparin/heparan sulfate with proteins: appraisal of structural factors and experimental approaches. (research.com)
Of the three tail spikes, two have protein domains associated with the pectate lyase family of proteins (Tsp2) and P22 tail spike family (Tsp3) with the prospect that these enable Salmonella O antigen degradation. (biomedcentral.com)

Tyrosine ammonia lyase (EC 4.3.1.23, L-tyrosine ammonia-lyase, TAL or Tyrase) is an enzyme in the natural phenols biosynthesis pathway. (wikipedia.org)
T A L {\displaystyle {\xrightarrow {TAL}}} + Ammonia + H+ L-tyrosine = trans-p-hydroxycinnamate + NH3 EC 4.3.1.24 (phenylalanine ammonia-lyase) EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase) Louie GV, Bowman ME, Moffitt MC, Baiga TJ, Moore BS, Noel JP (December 2006). (wikipedia.org)
Introduction of these transcription factors under control of the fruit specific E8 promoter increased the expression of most of the structural genes in the biosynthetic pathway in the tomato fruit, including phenylalanine ammonia lyase, chalcone isomerase and F35H. (chk1inhibitor.com)

Hydrolase breaks the α-1,4 glycosidic bond of the pectin polymer main chain, while lyase breaks the main chain by trans-elimination, creating an unsaturated bond at the non-reducing end (Fu et al. (springeropen.com)

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)
Schnicker, N.J., Dey, M. (2016) Bacillus anthracis Prolyl 4-Hydroxylase Modifies Collagen-like Substrates in Asymmetric Patterns. (uiowa.edu)

Dey, M., Rao, C. P., Guionneau, P. (2005) Structural characterization and reactivity of Cu(II) complex of p -tert-butyl-calix[4]arene bearing two imine pendants at lower rim. (uiowa.edu)
The structural biology group solved the structures of an SCO called NOV1 in an apo-form ( PDB ID 5J53 ), in complex with its substrate resveratrol ( PDB ID 5J54 ) and its product vanillin ( PDB ID 5J55 ). (jbei.org)
A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity [ 8 ]. (cazypedia.org)

The region PB2-T2-PB3 is the best conserved region in the lyases andshows the clearest structural similarity. (embl.de)
The sequence similarity among these different repeats or domains is low, however they exhibit considerable structural similarity. (eu.org)
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)

From 80 to 300 s structures show a mixture of decreasing substrate and increasing product of the nucleotidyl-transfer reaction. (proteopedia.org)
New Mechanistic Insight from Substrate-and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ. (uiowa.edu)
More recently we have probed the allosteric regulation of class II and class III RNRs by solving the structures of complexes with several combinations of allosteric effector and substrate [2,5]. (lu.se)
The structural biology group of JBEI in collaboration with Great Lakes Bioenergy solved the x-ray crystal structures of the glutathione-dependent β-etherases, LigE (PDB IDs 4YAM 4YAN ) and LigF (PDB ID 4XT0 ). (jbei.org)
Lastly, both structures reveal details on the conformational changes provoked by PLP binding that suggest an induced fit of the active site "entrance door", necessary to accommodate PLP and substrate molecules. (unipr.it)
Components of those structures show powerful resemblance to Cip1, indicating that Cip1 may have lyase activity. (ezh2inhibitor.com)

Isolation and Assays of Bacterial Dimethylsulfoniopropionate Lyases. (uiowa.edu)

In Advances in protein chemistry and structural biology (Vol. 109, pp. 195-222). (uiowa.edu)
Structural biology group provides molecular insights into specific interactions of EilR with its operator ( PDB ID 5VL9 ) and with two inducers, crystal violet ( PDB ID 5VLM ) and malachite green ( PDB ID 5VLG ). (jbei.org)
Structural Biology - Structural Characterization of the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. (jbei.org)
Our research involves a combination of molecular biology, protein biochemistry, organic synthesis and structural studies and provides a strong training for students interested in understanding the organic chemistry of living systems and in pursuing careers in biotechnology, drug design or academia. (tamu.edu)

This is the first structure of a polygalacturonase andcomprises a 10 turn right-handed parallel beta-helix domain with two loopregions forming a "tunnel like" substrate-binding cleft. (embl.de)
The structure of exopolygalacturonase from Yersinia enterocolitica shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase [ 8 ]. (cazypedia.org)

Based on docking studies and molecular dynamics simulations of the protein structure and a chondroitin substrate, we suggest a novel mechanism of DS-epi1, involving a His/double-Tyr motif. (scilifelab.se)
The authors then performed structural relaxation on six encounter complexes using "soluble" molecular dynamics (MD) simulations, which are MD simulations that were conducted in aqueous solution. (biologists.com)
A recent molecular and functional examination of the mutational effects showed that, although some mutations affect both substrate affinity and efficiency of the reaction, others affect one more than the other. (medscape.com)

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)
Particular emphasis is placed on classifications based on formal structural change and on reaction mechanism, and on the role of classifications within computerized reaction retrieval systems. (researchgate.net)
Based on substrates and mechanism of action, pectinase is classified into the following sub-types: protopectinase, pectinesterase, and depolymerase (Kashyap et al. (springeropen.com)
Dey, M., Li, X., Kunz, R.C., Ragsdale, S. W. (2010) Organometallic and Radical Intermediates in the Catalytic Mechanism of Methyl-Coenzyme M Reductase using the natural substrate methyl-coenzyme M and a Coenzyme B substrate analog. (uiowa.edu)
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)

A comprehensive analysis of the overall chemistry of isomerase reactions based on bond changes, reaction centres and substrates and products revealed that isomerase reactions are chemically diverse and difficult to classify using a hierarchical system. (researchgate.net)
First, isomerases are more likely to evolve new functions in different EC primary classes, especially lyases (EC 4), rather than evolve to perform different isomerase reactions. (researchgate.net)

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)

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)
Through the introduction of a structural Zn2+ site, the thermal tolerance was increased by more than 10°C and was paralleled by an increase in the catalytic optimum temperature by more than 5°C. (jbei.org)

Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-bound DddK from the Prolific Marine Bacterium Pelagibacter. (uiowa.edu)
Brummett A. E., Schnicker N. J., Crider A., Todd J. D., Dey M. (2015) Biochemical, Kinetic, and Spectroscopic Characterization of Ruegeria pomeroyi DddW-A Mononuclear Iron-Dependent DMSP Lyase. (uiowa.edu)

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)

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)
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 alcohol consumption must be avoided in patients with HMG-CoA lyase deficiency. (biomedcentral.com)
3-Hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) lyase deficiency is a recessive autosomal hereditary disease described for the first time by Faull et al. (biomedcentral.com)

98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates (numerous lesser expressed cell-wall-associated hydrolases targeted peptidoglycan). (frontiersin.org)
It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in α-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with β-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases [ 5 ]. (cazypedia.org)

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)
The substrates and two Mg(2+) ions are aligned within 40 s, but the bond formation is not evident until 80 s. (proteopedia.org)

The information content of these techniques is often complementary and leads to a detailed information concerning the electronic, magnetic, and structural properties of metal centers imbedded in a large polypeptide macromolecule. (uga.edu)

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)

As well as playing an integral structural role, SLs act as potent signalling molecules involved in numerous cellular pathways having been implicated in cancer, inflammatory conditions and cardiovascular disease. (ed.ac.uk)

The enzyme 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) lyase catalyzes the terminal steps in ketone body generation and leucine degradation. (rcsb.org)
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)

1YDN: Crystal Structure of the HMG-CoA Lyase from Brucella melitensis, Northeast Structural Genomics Target LR35. (rcsb.org)
Second, isomerases change their overall chemistry and conserve the structure of their substrates and products more often than conserving the chemistry and changing substrates and products. (researchgate.net)
A comparison with a tryptophan-bound NosL structure suggests that substrate binding causes the closing of the first tunnel and, along with mutagenesis studies, that tyrosine binds to HydG with its amino group well positioned for H-abstraction by SAM. (nih.gov)

The lyase is highly specific toward α-1, 4-glucosidic bonds and shows negligible activity toward α-1, 6-glucosidic bonds. (go.jp)
Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. (proteopedia.org)
The activity of this enzyme is commonly assayed using a leucine arylamide chromogenic substrate such as leucyl beta-naphthylamide. (lookformedical.com)

α-Glucosidase contributing starch and glycogen metabolisms in plant and animal tissue is characterized by the variety in substrate recognition. (go.jp)

This was the first structural proof of a common evolutionary origin for the three classes of RNR and also pointed to an evolutionary relationship to the glycyl radical enzyme pyruvate formate lyase (PFL). (lu.se)

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)

In most other polysaccharide lyase mechanisms a proton donor has not been identified. (cazypedia.org)

When pre-treating the substrates with HPH, the release in orange peel was enhanced significantly leading to a POS content of 44.51â ¯g/100â ¯g peel, whereas oligosaccharide solubilization in apple bagasse was not affected. (bvsalud.org)

The production of citrate, the first substrate in the citric acid cycle, is limited, thus preventing the citric acid cycle from functioning, shown in the figure below. (medscape.com)
Hyaluronic acid was treated exhaustively with a hyaluronate lyase (hyaluronidase, EC 4.2.2.1) from Streptomyces hyalurolyticus to obtain a tetrasaccharide and a hexasaccharide product in a molar ratio of 1 to 1.2. (rpi.edu)
EC 4.8.1.5 , thiohydroximate- O -sulfate sulfate/sulfur-lyase (nitrile-forming) and EC 4.8.1.6 , N -(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming). (enzyme-database.org)
Compound 5 is fumaric acid generated in the reaction that converts ASA to arginine (6), which is mediated by ASA lyase. (medscape.com)

Each coil of the helix represents a structural repeat that, in some homologues, can be recognised from sequence information alone. (embl.de)

Similar movements were observed for the class III enzyme but the full picture has still not been obtained as substrates were not observed to bind to the active site in this system. (lu.se)
We continue to try to obtain substrate binding to the active site of class III RNRs. (lu.se)

Anatomy10

Organisms20

Chemicals and Drugs132

Analytical, Diagnostic and Therapeutic Techniques and Equipment28

Phenomena and Processes65

Technology, Industry, Agriculture1

Information Science5

Health Care3

Specificity5

Enzymes12

Heparin and heparan sulfate lyases1

Pectate lyases4

Specificities2

Polysaccharide lyase family2

Pectin lyase3

Proteins6

Ammonia-lyase3

HYDROLASE1

Bacillus2

Complex3

Similarity3

Structures6

Bacterial1

Biology4

Cleft2

Molecular3

Mechanism5

Isomerase2

DECARBOXYLASE1

Catalytic2

Biochemical2

Enzyme activity1

Deficiency4

Hydrolases2

Ions2

Polypeptide1

Amino acid1

Molecules1

Degradation2

Structure3

Activity3

Recognition1

Radical1

Cleavage1

Mechanisms1

Enhanced significantly1

Acid4

Represents a structural1

Active2