title: A method using active-site sequence conservation to find functional shifts in protein families: application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens.
abstract: We have introduced a method to identify functional shifts in protein families. Our method is based on the calculation of an active-site conservation ratio, which we call the "ASC ratio." For a structurally based alignment of a protein family, this ratio is the average sequence similarity of the active-site region compared to the full-length protein. The active-site region is defined as all the residues within a certain radius of the known functionally important groups. Using our method, we have analyzed enzymes of central metabolism from a large number of genomes (35). We found that for most of the enzymes, the active-site region is more highly conserved than the full-length sequence. However, for three tricarboxylic acid (TCA)-cycle enzymes, active-site sequences are considerably more diverged (than full-length ones). In particular, we were able to identify in six pathogens a novel isocitrate dehydrogenase that has very low sequence similarity around the active site. Detailed sequence-structure analysis indicates that while the active-site structure of isocitrate dehydrogenase is most likely similar between pathogens and nonpathogens, the unusual sequence divergence could result from an extra domain added at the N-terminus. This domain has a leucine-rich motif similar one in the Yersinia pestis cytotoxin and may therefore confer additional pathogenic functions.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Rajdeep
authors.initials: R
authors.lastname: Das
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002952:Citric Acid Cycle; D017124:Conserved Sequence; D006801:Humans; D007521:Isocitrate Dehydrogenase / Q000737:chemistry* / Q000378:metabolism*; D008291:Malate Dehydrogenase / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D013385:Succinate Dehydrogenase / Q000737:chemistry / Q000378:metabolism
chemical_list: D008291:Malate Dehydrogenase; D007521:Isocitrate Dehydrogenase; D013385:Succinate Dehydrogenase