Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases

FEBS Lett. 2002 Sep 25;528(1-3):114-8. doi: 10.1016/s0014-5793(02)03264-7.


The X-ray crystal structure has revealed two similar alpha/beta domains of aspartate racemase (AspR) from Pyrococcus horikoshii OT3, and identified a pseudo mirror-symmetric distribution of the residues around its active site [Liu et al. (2002) J. Mol. Biol. 319, 479-489]. Structural homology and functional similarity between the two domains suggested that this enzyme evolved from an ancestral domain by gene duplication and gene fusion. We have expressed solely the C-terminal domain of this AspR and determined its three-dimensional structure by X-ray crystallography. The high structural stability of this domain supports the existence of the ancestral domain. In comparison with other amino acid racemases (AARs), we suggest that gene duplication and gene fusion are conventional ways in the evolution of pyridoxal 5'-phosphate-independent AARs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Isomerases / chemistry*
  • Amino Acid Isomerases / genetics*
  • Amino Acid Isomerases / metabolism
  • Amino Acid Sequence
  • Artificial Gene Fusion
  • Base Sequence
  • Crystallography, X-Ray
  • DNA, Bacterial / genetics
  • Enzyme Stability
  • Evolution, Molecular*
  • Gene Duplication
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • Pyridoxal Phosphate / metabolism
  • Pyrococcus / enzymology
  • Pyrococcus / genetics
  • Sequence Homology, Amino Acid


  • DNA, Bacterial
  • Pyridoxal Phosphate
  • Amino Acid Isomerases
  • aspartate racemase