Structure of putrescine aminotransferase from Escherichia coli provides insights into the substrate specificity among class III aminotransferases

PLoS One. 2014 Nov 25;9(11):e113212. doi: 10.1371/journal.pone.0113212. eCollection 2014.


YgjG is a putrescine aminotransferase enzyme that transfers amino groups from compounds with terminal primary amines to compounds with an aldehyde group using pyridoxal-5'-phosphate (PLP) as a cofactor. Previous biochemical data show that the enzyme prefers primary diamines, such as putrescine, over ornithine as a substrate. To better understand the enzyme's substrate specificity, crystal structures of YgjG from Escherichia coli were determined at 2.3 and 2.1 Å resolutions for the free and putrescine-bound enzymes, respectively. Sequence and structural analyses revealed that YgjG forms a dimer that adopts a class III PLP-dependent aminotransferase fold. A structural comparison between YgjG and other class III aminotransferases revealed that their structures are similar. However, YgjG has an additional N-terminal helical structure that partially contributes to a dimeric interaction with the other subunit via a helix-helix interaction. Interestingly, the YgjG substrate-binding site entrance size and charge distribution are smaller and more hydrophobic than other class III aminotransferases, which suggest that YgjG has a unique substrate binding site that could accommodate primary aliphatic diamine substrates, including putrescine. The YgjG crystal structures provide structural clues to putrescine aminotransferase substrate specificity and binding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Crystallography, X-Ray
  • Dimerization
  • Escherichia coli / enzymology*
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Denaturation
  • Putrescine / metabolism*
  • Pyridoxal Phosphate / metabolism
  • Sequence Homology, Amino Acid
  • Substrate Specificity
  • Transaminases / chemistry*
  • Transaminases / metabolism


  • Pyridoxal Phosphate
  • Transaminases
  • Putrescine

Associated data

  • PDB/4UOX
  • PDB/4UOY

Grant support

This work was supported by the Basic Science Research Program of the National Research Foundation of Korea (NRF), which is funded by the Ministry of Education, Science and Technology (grant 2011-0007201) and by the Marine Extreme Genome Research Center Program of the Ministry of Land, Transport and Maritime Affairs.