Trends in Biochemical Sciences
Protein Sequence MotifA conserved domain in prokaryotic bifunctional FAD synthetases can potentially catalyze nucleotide transfer
Section snippets
Recognition of the N-terminal domain
Using the non-redundant database (NRDB), PSI-BLAST [9] (http://www.ncbi.nlm.nih.gov/blast/) searches have identified N-terminal region homologues of various bifunctional FAD synthetases. Many different homologous sequences of the N-terminal region of FAD synthetases have been used as queries in various PSI-BLAST searches. In the first iteration, the homologues that were identified included bacterial RibF gene products involved in FAD synthesis (E values: 3×10−86–3×10−4). Sequences of >30
Similarities between the N-terminal domain and nucleotidyl transferases
Subsequent PSI-BLAST searches of NRDB, using the N-terminal domain of bacterial FAD synthetases as the query, identified homologues of nucleotidyl transferases (E values: <4×10−4). These homologues included bacterial nucleotidyl transferases and their homologues from human cells, Arabidopsis thaliana and other eukaryotic sources that share a low sequence similarity (<20%) with the N-terminal domain of FAD synthetases. No other family of eukaryotic proteins was identified as related to the
Conservation of substrate-binding motifs
Multiple sequence alignment of N-terminal domains of the bifunctional FAD synthetases with the nucleotidyl transferase phosphopantetheine adenylyl transferase (PPAT, PDB code: 1b6t) has revealed conservation of two distantly spaced His-Xaa-Gly-His and Ser/Thr-rich motifs in the primary structure (Fig. 1). Both these motifs are known to interact with the nucleotide [15]. The glycine and histidine residues are part of the adenine-binding pocket, whereas the two serine residues in the second
Conclusions
The N-terminal region of bifunctional FAD synthetases has been identified as a domain that is related to nucleotidyl transferases using various computational methods, and is implicated in the adenylylation of FMN. Conservation of the two key motifs that are involved in the catalysis of the nucleotidyl transferases suggests a similar role for these residues in bacterial FAD synthesis. The two distinct functions of bacterial FAD synthetases that lead to FAD formation are, therefore, localized to
Acknowledgements
A.K. and K.S. are supported by Council of Scientific and Industrial Research, New Delhi, India. This research is supported by the award of International Senior Fellowship by the Wellcome Trust, London (UK), and the Computational Genomics project by Dept of Biotechnology, New Delhi to N.S., and by [DST/INT/US/NSF(RP-026)] Indo-USA Collaboration, by Department of Science and Technology, New Delhi, to S.J.
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