title: Phylogenetic analysis of condensation domains in the nonribosomal peptide synthetases.
abstract: Condensation (C) domains in the nonribosomal peptide synthetases are capable of catalyzing peptide bond formation between two consecutively bound various amino acids. C-domains coincide in frequency with the number of peptide bonds in the product peptide. In this study, a phylogenetic approach was used to investigate structural diversity of bacterial C-domains. Phylogenetic trees show that the C-domains are clustered into three functional groups according to the types of substrate donor molecules. They are l-peptidyl donors, d-peptidyl donors, and N-acyl donors. The fact that C-domain structure is not subject to optical configuration of amino acid acceptor molecules supports an idea that the conversion from l to d-form of incorporating amino acid acceptor occurs during or after peptide bond formation. l-peptidyl donors and d-peptidyl donors are suggested to separate before separating the lineage of Gram-positive and Gram-negative bacteria in the evolution process.
authors.affiliation: Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan.
authors.forename: Niran
authors.initials: N
authors.lastname: Roongsawang
authors.forename: Siew Ping
authors.initials: SP
authors.lastname: Lim
authors.forename: Kenji
authors.initials: K
authors.lastname: Washio
authors.forename: Kazufumi
authors.initials: K
authors.lastname: Takano
authors.forename: Shigenori
authors.initials: S
authors.lastname: Kanaya
authors.forename: Masaaki
authors.initials: M
authors.lastname: Morikawa
mesh_terms: D000595:Amino Acid Sequence; D006090:Gram-Negative Bacteria / Q000201:enzymology* / Q000235:genetics; D006094:Gram-Positive Bacteria / Q000201:enzymology* / Q000235:genetics; D008969:Molecular Sequence Data; D046908:Peptide Biosynthesis, Nucleic Acid-Independent; D010453:Peptide Synthases / Q000737:chemistry* / Q000235:genetics*; D010455:Peptides / Q000737:chemistry; D010802:Phylogeny; D011487:Protein Conformation; D013379:Substrate Specificity
chemical_list: D010455:Peptides; D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase