Identification of a new nucleotide binding site by structural alignment and site directed mutagenesis

Proteins
Xiaoying ZhangZongchao Jia

Abstract

Nucleotide binding proteins are involved in many important cellular processes and form one of the largest protein families. Traditionally, the identification of nucleotide binding motif, such as the ATP binding P-loop, has relied on the comparison of protein sequences, consideration of the function of each of the proteins and the identification of signature motifs within the sequence. Sometimes, it is difficult to identify nucleotide binding proteins based on sequence alignment because of increased evolutionary distances. In such cases, structural alignments can provide a better guide for comparing specific features of sequences because the overall structures of these motifs are conserved despite low sequence identity. In the present study, on the basis of bioinformatics and structural comparison of three representative protein structures of Ham1 superfamily, YjjX, YggV, and YhdE, previously identified as nucleotide binding proteins, we have identified a novel nucleotide binding motif (T/SXXXXK/R). The importance of this signature motif in binding of nucleotides was validated using site directed mutagenesis. Mutations of conserved residues of the loop either decreased or completely abolished the nucleotide binding activity of t...Continue Reading

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