Open AccessPhylogenetic analysis of condensation domains in the nonribosomal peptide synthetases
Author(s) -
Roongsawang Niran,
Lim Siew Ping,
Washio Kenji,
Takano Kazufumi,
Kanaya Shigenori,
Morikawa Masaaki
Publication year - 2005
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1016/j.femsle.2005.08.041
Subject(s) - nonribosomal peptide , peptide , peptide bond , phylogenetic tree , amino acid , stereochemistry , biology , molecule , peptide sequence , chemistry , biochemistry , biosynthesis , enzyme , organic chemistry , gene
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.