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.
Bibliographical noteFunding Information:
This work was supported by a Grant 311042-05-1-HD120 from the Korea Institute of Planning & Evaluation for Technology (iPET) funded by the Ministry for Food, Agriculture, Forestry and Fisheries to Dr. Dong-Woo Lee, and by research funds from Chosun University (2008) to Dr. Sung Haeng Lee.
All Science Journal Classification (ASJC) codes
- Structural Biology
- Molecular Biology
- Cell Biology