title: Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway.
abstract: Salicylaldehyde (SAL) dehydrogenase (SALD) is responsible for the oxidation of SAL to salicylate using nicotinamide adenine dinucleotide (NAD+) as a cofactor in the naphthalene degradation pathway. We report the use of a protein sequence similarity network to make functional inferences about SALDs. Network and phylogenetic analyses indicated that SALDs and the homologues are present in bacteria and fungi. The key residues in SALDs were analyzed by evolutionary methods and a molecular simulation analysis. The results showed that the catalytic residue is most highly conserved, followed by the residues binding NAD+and then the residues binding SAL. A molecular simulation analysis demonstrated the binding energies of the amino acids to NAD+and/or SAL and showed that a conformational change is induced by binding. A SALD from Alteromonas naphthalenivorans (SALDan) that undergoes trimeric oligomerization was characterized enzymatically. The results showed that SALDan could catalyze the oxidation of a variety of aromatic aldehydes. Site-directed mutagenesis of selected residues binding NAD+and/or SAL affected the enzyme's catalytic efficiency, but did not eliminate catalysis. Finally, the relationships among the evolution, catalytic mechanism, and functions of SALD are discussed. Taken together, this study provides an expanded understanding of the evolution, functions, and catalytic mechanism of SALD.
authors.affiliation: School of Bioengineering, Qilu University of Technology, Jinan 250353, China.|Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
authors.forename: Baolei
authors.initials: B
authors.lastname: Jia
authors.affiliation: Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
authors.forename: Xiaomeng
authors.initials: X
authors.lastname: Jia
authors.affiliation: Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
authors.forename: Kyung
authors.initials: K
authors.lastname: Hyun Kim
authors.affiliation: School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Ji Pu
authors.affiliation: Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea.
authors.forename: Myung-Suk
authors.initials: MS
authors.lastname: Kang
authors.affiliation: Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
authors.forename: Che
authors.initials: C
authors.lastname: Ok Jeon
mesh_terms: D000445:Aldehyde Oxidoreductases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D005658:Fungi / Q000145:classification / Q000235:genetics / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D009281:Naphthalenes / Q000737:chemistry / Q000378:metabolism*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013379:Substrate Specificity
chemical_list: D009281:Naphthalenes; D000445:Aldehyde Oxidoreductases; C024246:salicylaldehyde dehydrogenase