title: Structural insights into conserved L-arabinose metabolic enzymes reveal the substrate binding site of a thermophilic L-arabinose isomerase.
abstract: Structural genomics demonstrates that despite low levels of structural similarity of proteins comprising a metabolic pathway, their substrate binding regions are likely to be conserved. Herein based on the 3D-structures of the α/β-fold proteins involved in the ara operon, we attempted to predict the substrate binding residues of thermophilic Geobacillus stearothermophilus L-arabinose isomerase (GSAI) with no 3D-structure available. Comparison of the structures of L-arabinose catabolic enzymes revealed a conserved feature to form the substrate-binding modules, which can be extended to predict the substrate binding site of GSAI (i.e., D195, E261 and E333). Moreover, these data implicated that proteins in the l-arabinose metabolic pathway might retain their substrate binding niches as the modular structure through conserved molecular evolution even with totally different structural scaffolds.
authors.affiliation: School of Applied Biosciences, Kyungpook National University, Daegu 702-701, South Korea.
authors.forename: Yong-Jik
authors.initials: YJ
authors.lastname: Lee
authors.affiliation: School of Applied Biosciences, Kyungpook National University, Daegu 702-701, South Korea.
authors.forename: Sang-Jae
authors.initials: SJ
authors.lastname: Lee
authors.affiliation: CJ Foods R&D, CJ Cheiljedang Corporation, Seoul, South Korea.
authors.forename: Seong-Bo
authors.initials: SB
authors.lastname: Kim
authors.affiliation: Infection & Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, South Korea.
authors.forename: Sang Jun
authors.initials: SJ
authors.lastname: Lee
authors.affiliation: Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 501-759, South Korea. Electronic address: sunglee@chosun.ac.kr.
authors.forename: Sung Haeng
authors.initials: SH
authors.lastname: Lee
authors.affiliation: School of Applied Biosciences, Kyungpook National University, Daegu 702-701, South Korea. Electronic address: leehicam@knu.ac.kr.
authors.forename: Dong-Woo
authors.initials: DW
authors.lastname: Lee
mesh_terms: D019747:Aldose-Ketose Isomerases / Q000737:chemistry* / Q000235:genetics; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D020134:Catalytic Domain; D017124:Conserved Sequence; D004926:Escherichia coli / Q000201:enzymology; D001411:Geobacillus stearothermophilus / Q000201:enzymology*; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020836:Protein Structure, Quaternary; D020124:Thermotoga maritima / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D019747:Aldose-Ketose Isomerases; C019715:L-arabinose isomerase
keywords: Prediction; Structural genomics; Substrate binding site; Thermophilic; l-Arabinose isomerase