Cho, Hoon Choi, Cheol-Hee Yoo, Kyung Ho Cho, Seung Joo 2024-01-20T22:04:26Z 2024-01-20T22:04:26Z 2021-09-03 2008-12-31 1738-642X https://pubs.kist.re.kr/handle/201004/132861 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 a-hydrogen of beta-mannuronate, which was suitable to initiate a beta-elimination reaction. K347 was also very near to the carboxylate moiety 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. English KOREAN SOCIETY TOXICOGENOMICS & TOXICOPROTEOMICS-KSTT MUCOID PSEUDOMONAS-AERUGINOSA TUMEFACIENS STRAIN C58 ALGINATE LYASE ATU3025 A Molecular Modeling Study of AAD16034 Article 1 MOLECULAR & CELLULAR TOXICOLOGY, v.4, no.4, pp.307 - 310 MOLECULAR & CELLULAR TOXICOLOGY 4 4 307 310 scie kci other 000262121900006 Biochemistry & Molecular Biology Toxicology Biochemistry & Molecular Biology Toxicology Article MUCOID PSEUDOMONAS-AERUGINOSA TUMEFACIENS STRAIN C58 ALGINATE LYASE ATU3025 Homology modeling Docking Alginate lyase AAD16034