title: Isoprenyl diphosphate synthases: protein sequence comparisons, a phylogenetic tree, and predictions of secondary structure.
abstract: Isoprenyl diphosphate synthases are ubiquitous enzymes that catalyze the basic chain-elongation reaction in the isoprene biosynthetic pathway. Pairwise sequence comparisons were made for 6 farnesyl diphosphate synthases, 6 geranylgeranyl diphosphate synthases, and a hexaprenyl diphosphate synthase. Five regions with highly conserved residues, two of which contain aspartate-rich DDXX(XX)D motifs found in many prenyltransferases, were identified. A consensus secondary structure for the group, consisting mostly of alpha-helices, was predicted for the multiply aligned sequences from amino acid compositions, computer assignments of local structure, and hydropathy indices. Progressive sequence alignments suggest that the 13 isoprenyl diphosphate synthases evolved from a common ancestor into 3 distinct clusters. The most distant separation is between yeast hexaprenyl diphosphate synthetase and the other enzymes. Except for the chromoplastic geranylgeranyl diphosphate synthase from Capsicum annuum, the remaining farnesyl and geranylgeranyl diphosphate synthases segregate into prokaryotic/archaebacterial and eukaryotic families.
authors.affiliation: Department of Chemistry, University of Utah, Salt Lake City 84112.
authors.forename: A
authors.initials: A
authors.lastname: Chen
authors.forename: P A
authors.initials: PA
authors.lastname: Kroon
authors.forename: C D
authors.initials: CD
authors.lastname: Poulter
mesh_terms: D019883:Alkyl and Aryl Transferases; D000595:Amino Acid Sequence; D000818:Animals; D001419:Bacteria / Q000201:enzymology; D001665:Binding Sites; D002645:Chickens; D017124:Conserved Sequence; D004122:Dimethylallyltranstransferase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D051231:Farnesyltranstransferase; D051228:Geranyltranstransferase; D006801:Humans; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009492:Neurospora crassa / Q000201:enzymology; D010802:Phylogeny; D010944:Plants / Q000201:enzymology; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D016415:Sequence Alignment; D014166:Transferases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D014166:Transferases; D019883:Alkyl and Aryl Transferases; D004122:Dimethylallyltranstransferase; D051228:Geranyltranstransferase; D051231:Farnesyltranstransferase; C036826:trans-pentaprenyltranstransferase