Crystal structure analysis of l-fuculose-1-phosphate aldolase from Thermus thermophilus HB8 and its catalytic action: as explained through in silico

• Published in: Journal of structural and functional genomics Vol. 14; no. 2; pp. 59 - 70
• Main Authors: Karthik, L., Nachiappan, M., Velmurugan, D., Jeyakanthan, J., Gunasekaran, K.
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.06.2013; Springer Nature B.V
• Subjects: Aldehyde-Lyases - chemistry; Aldehyde-Lyases - metabolism; Amino Acid Sequence; Amino acids; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Catalysis; Catalytic Domain; Computer Simulation; Crystal structure; Crystallography, X-Ray; Data collection; Dihydroxyacetone Phosphate - metabolism; E coli; Enzymes; Escherichia coli; Escherichia coli - enzymology; Escherichia coli - metabolism; Forestry Management; Human Genetics; Hydroxamic Acids - chemistry; Hydroxamic Acids - metabolism; Life Sciences; Ligands; Microbial Genetics and Genomics; Models, Molecular; Molecular Sequence Data; Plant Genetics and Genomics; Protein Conformation; Proteins; Thermus thermophilus; Thermus thermophilus - enzymology; Thermus thermophilus - metabolism; Yeast; Zinc; Induced fit docking; Dihydroxyacetone phosphate; Class II aldolase; Fuculose phosphate aldolase; Fuculose-1-phosphate; HB8
• ISSN: 1345-711X; 1570-0267
• DOI: 10.1007/s10969-013-9156-8

Fuculose phosphate aldolase catalyzes the reversible cleavage of fuculose-1-phosphate to dihydroxyacetone phosphate and l -lactaldehyde. A tetramer by nature, this enzyme from Thermus thermophilus HB8 represents the group of Class II aldolases. The structure was solved in two different space groups using the crystals obtained from slow evaporation vapour-diffusion and microbatch techniques. The detailed crystallization description has been reported previously. In this study, the structural features of fuculose phosphate aldolase from T. thermophilus have been explored extensively through sequence and structure comparisons with fuculose phosphate aldolases of different species. Finally, an in silico analysis using induced fit docking was attempted to deduce the binding mode of fuculose phosphate aldolase with its natural substrate fuculose-1-phosphate along with a substrate analog dihydroxyacetone phosphate and phosphoglycolohydroxymate—a potential aldolase inhibitor. The results show the mechanism of action may be similar to that of Escherichia coli fuculose aldolase.