Phylogenetic analysis of condensation domains in the nonribosomal peptide synthetases.
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.
Roongsawang
Niran
N
Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan.
Lim
Siew Ping
SP
Washio
Kenji
K
Takano
Kazufumi
K
Kanaya
Shigenori
S
Morikawa
Masaaki
M
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
D010455:Peptides; D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase