• Proceedings of the Korean Society of Life Science Conference
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• 2006.09a
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• pp.85.2-85.2
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• 2006

• Molecular & Cellular Toxicology
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• v.4 no.4
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• pp.307-310
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• 2008

AAD16034 is an alginate lyase from Pseudoalteromonas sp. IAM14594. A very close homologue with known 3D structure exists (marine bacterium Pseudoalteromonas sp. strain no. 272). A three-dimensional structure of AAD16034 was generated based on this template (PDB code: 1J1T) by comparative modeling. The modeled enzyme exhibited a jelly-roll like structure very similar to its template structure. Both enzymes possess the characteristic alginate sequence YFKhG+Y-Q. Since AAD16034 displays enzymatic activity for poly-M alginate, docking of a tri-mannuronate into the modeled structure was performed. Two separate and adjacent binding sites were found. The ligand was accommodated inside each binding site. By considering both binding sites, a plausible binding pose for the poly-M alginate polymer could be deduced. From the modeled docking pose (i.e., the most important factor that attracts alginate polymer into this lyase) the most likely interaction was electrostatic. In accordance with a previous report, the hydroxyl group of Y345 was positioned close to the ${\alpha}$-hydrogen of ${\beta}$-mannuronate, which was suitable to initiate a ${\beta}$-elimination reaction. K347 was also very near to the carboxylatemoiety of the ligand, which might stabilize the dianion intermediate during the ${\beta}$-elimination reaction. This implies that the characteristic alginate sequence is absolutely crucial for the catalysis. These results may be exploited in the design of novel enzymes with desired properties.

• Journal of Integrative Natural Science
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• v.3 no.2
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• pp.72-77
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• 2010

Alginate lyases, also known as alginases or alginate depolymerases, catalyze the degradation of alginate by a ${\beta}$-elimination mechanism that has yet to be fully elucidated. Alginate is a copolymer of ${\alpha}$-L-guluronate (G) and its C5 epimer ${\beta}$-D-mannuronate (M), arranged as homopolymeric G blocks, M blocks, alternating GM or random heteropolymeric G/M stretches. Almost all alginate lyases depolymerize alginate in an endolytical fashion via a ${\beta}$-elimination reaction. The alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, consisting of 776 amino-acid residues, is a novel exotype alginate lyase classified into polysaccharide lyase family 15. Till now there is no crystal structure available for this class of proteins. Since there is no template with high sequence identity, three-dimensional coordinates for exotype alginate lyase (PL 15 family) were determined using modeling methods (Comparitive modeling and Fold recognition). The structures were modeled using the X-ray coordinates from Heparinase protein family (PDB code: 3E7J). This enzyme (Atu3025) displays enzymatic activity for both poly-M and poly-G alginate. Since poly-M is widespread; docking of a tri-mannuronate against the modeled structure was performed. We identified some of those residues which are crucial for lyase activity. The results from this study should guide future mutagenesis studies and also provides a starting point for further proceedings.

• Journal of Life Science
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• v.19 no.1
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• pp.34-39
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• 2009

Alginate with a MW of 1,283 kDa was hydrolyzed with 0.4 M organic acids at $100^{\circ}C$ for 3 hr. Molecular weights of alginates hydrolyzed with organic acids ranged from 7.5 to 53.2 kDa. There was no significant difference in the molar ratio of mannuronate to guluronate in alginates hydrolyzed with organic acids. Acetic add was found to be the most effective organic acid for hydrolysis of alginate. The MW of alginate decreased with increasing concentration and reaction time with acetic acid as a hydrolyzing agent. The correlations between the MW of hydrolyzed alginate and concentration of acetic acid as well as reaction time with 0.4 M acetic acid were plotted and the relevant equations obtained in this study. Polymannuronate and polyguluronate were isolated by pH adjustment of alginate hydrolyzed with 0.4 M acetic add. The molar percentages of mannuronate in polymannuronates isolated from alginate hydrolyzed with 0.4 M acetic acid at $100^{\circ}C$ were increasing in proportional to the reaction time such as 75% for 1 hr, 90% for 3 hr, and 98% for 5 hr of reaction time.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.33 no.4
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• pp.325-330
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• 2000

Alginate obtained from brown algae had various physicochemical and rheological properties and could used as a dietary fiber, However, alginate has not been widely applied to the food industry, since it had high viscosity, high gelling effect conjugated with some mineral, and low solubility. To improve functionality of alginate, partially develymerized alginates, which was water-soluble dietary fiber were obtained by hydrolysis of alginate from the sea tangle, Laminaria japonicus, heated at $121^{\circ}C$. Effects of depolymerization of alginate on the changes of viscosity and average molecular weight, block composition ratio of mannuronate to guluronate (M/G ratio), chemical properties using $PT-IR, ^1H-NMR, and ^(13)C-NMR$ spectrum were investigated. The average molecular weight and viscosity of the alginate were rapidly decreased with the thermal decomposition, and estimated to be 1,307,415 dalton and 284,000 cps, before heating, 728,106 and 3,940.29 cps after 30 min heating, 102,635 and 22.22 cps after 2.5 hrs heating, 51,205 and 12.05 cps after 3 hrs, and 10,049 and 4.28 cps after 6.5 hrs, respectively. The M/G ratio was increased with the heating time, while MM-block did not show any changes and GG-block diminished. The results of $FT-IR, ^1H-NMR and ^(13)C-NMR$ spectrum suggested that changes of molecular structure did not occur by the thermal decomposition.

• Journal of Life Science
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• v.17 no.5 s.85
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• pp.625-633
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• 2007

We isolated a new extracellular alginate lyase-producing microorganism, which displayed alginate-depolymerizing activity in plate assays, from coastal soils in Wando, Jeollanam-do, Korea. This alginate-depolymerizing bacterium belonged to the genus Streptomyces and it was named Streptomyces sp. MET 0515. An extracellular alginate lyase(ALY1) secreted by Streptomyces sp. MET 0515, was purified to homogeneity by a combination of acetone precipitation, anion-exchange chromatography (Q-Sepharose and DEAE-Sepharose) and Sephacryl S-200 HR gel filtration chromatography. Its molecular mass was 26 kDa as determined by SDS-PACE analysis. The enzyme had an optimal temperature of $70^{\circ}C$ for its activity, and was most active at pH 7.5. The thermal and pH stability were $0-50^{\circ}C$, and pH 6.0-9.0, respectively. The enzyme activity was stimulated by 1mM $Mn^{2+}$, and inhibited by 1mM $Fe^{3+}$, 1mM EDTA and 1mM $Zn^{2+}$. Preliminary analysis of substrate specificity showed that this alginate lyase had activity on both poly-alpha 1,4-L-guluronate and poly-beta 1,4-D-mannuronate in the alginate molecule.

• Journal of Life Science
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• v.15 no.6 s.73
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• pp.857-862
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• 2005

This study investigated the proliferation and DNA synthesis inhibitory effect of concentrations ($0.01\%$, $0.1\%$, $0.25\%$, $0.5\%$) when added whole molecular-, 40 kDa-, or 10 kDa polymannuronate on human colon cancer cells, HT-29, DLD-1, and WiDr, in vitro. In order to determine the proliferation inhibitory effect of low-molecularized polymannuronate, the treatment of whole molecular-, 40 kDa-, 10 kDa-, polymannuronate ($0.25\%$) to the HT-29 cancer cells inhibited proliferation of cancer cells by $41\%$, $69.1\%$, and $75.6\%$, respectively. DLD-1 cancer cell was not relation of molecular weight and concentration. WiDr cancer cell depend on concentration without molecular weight. In addition, whole molecular-, 40 kDa-, 10 kDa poly mannuronate ($0.25\%$) significantly inhibited DNA synthesis of HT-29 cancer .cells by $78\%$, $58\%$, and $56\%$, respectively. And morphological changes not found under microscope by polymannuronate. Therefore polymannuronate would be helpful to colon cancer treatment as well as cancer prevention and this study would be the basic source for further research of polymannuronate.

• Journal of Life Science
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• v.25 no.2
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• pp.121-129
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• 2015

Alginates are found in marine brown seaweeds and in extracellular biofilms secreted by some bacteria. Previously, we reported an oligoalginate lyase from Sphingomonas sp. MJ-3 (MJ3-Oal) that had an exolytic activity and protein sequence homology with endolytic polymannuronate (polyM) lyase in the N-terminal region. In this study, the MJ3-Oal was tested for both exolytic and endolytic activity by homology modeling using the crystal structure of Alg17c from Saccharophagus degradans 2-40T. The tyrosine residue at the $426^{th}$ position, which possibly formed a hydrogen bond with the substrate, was mutated to phenylalanine. The FPLC profiles showed that MJ3-Oal degraded alginate quickly to monomers as a final product through the oligmers, whereas the Tyr426Phe mutant showed only exolytic alginate lyase activity. $^1H$-NMR spectra also showed that MJ3-Oal degraded the endoglycosidic bond of polyM and polyMG (polymannuronate-guluronate) blocks. These results indicate that oligoalginate lyase from Sphingomonas sp. MJ-3 probably catalyzes the degradation of both exo- and endo-glycosidic bonds of alginate.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.31 no.1
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• pp.82-89
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• 1998

Partial hydrolyzing condition for low-molecularized alginate and rheological properties such as viscosity, solubility, emulsitying ability, oil absorption capacity, bile acids binding and metal ion binding of the low-molecularized alginates from the sea mustard ( Undaria pinnatifida) and giant kelp (Macrocystis pyrifera) were investigated. Alginate from sea mustard was regularly hydrolyzed with the increase of HCl concentration in the range of 0.2 N to 0.5 N and with the prolonged reaction time at $100^{\circ}C$. The molecular weight of alginate was decreased to a part of 100 after hydrolysis for 50 min with 0.3 N HCl. The ratio of mannuronate to guluronate was increased with the acid hydrolysis and total yield was estimated to be $75\%\~80\%$. Low-molecularization of alginate was featured in the apparent decrease of viscosity, whereas solubility, emulsifying ability, and bile acids binding ability were increased with the low-molecularization. Oil absorption capacity of the acid$\cdot$alkali soluble alginate was slightly higher than that of the water soluble alginate. Metal ion binding capacity was the highest in acid$\cdot$alkali soluble alginate, and decreased with the low-molecularization.