Structure of ALD1, a plant-specific homologue of the universal diaminopimelate aminotransferase enzyme of lysine biosynthesis

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Feb 1;69(Pt 2):84-9. doi: 10.1107/S1744309112050270. Epub 2013 Jan 26.

Abstract

Diaminopimelate aminotransferase (DAP-AT) is an enzyme in the lysine-biosynthesis pathway. Conversely, ALD1, a close homologue of DAP-AT in plants, uses lysine as a substrate in vitro. Both proteins require pyridoxal-5'-phosphate (PLP) for their activity. The structure of ALD1 from the flowering plant Arabidopsis thaliana (AtALD1) was solved at a resolution of 2.3 Å. Comparison of AtALD1 with the previously solved structure of A. thaliana DAP-AT (AtDAP-AT) revealed similar interactions with PLP despite sequence differences within the PLP-binding site. However, sequence differences between the binding site of AtDAP-AT for malate, a purported mimic of substrate binding, and the corresponding site in AtALD1 led to different interactions. This suggests that either the substrate itself, or the substrate-binding mode, differs in the two proteins, supporting the known in vitro findings.

Keywords: Arabidopsis thaliana; DAP-AT; LPC/CSU analysis; PLP binding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Arabidopsis / enzymology*
  • Arabidopsis Proteins / chemistry*
  • Binding Sites
  • Coenzymes / metabolism
  • Crystallography, X-Ray
  • Diaminopimelic Acid / metabolism*
  • Lysine / biosynthesis*
  • Molecular Sequence Data
  • Pyridoxal Phosphate / metabolism
  • Sequence Alignment
  • Species Specificity
  • Structural Homology, Protein*
  • Substrate Specificity
  • Transaminases / chemistry*

Substances

  • Arabidopsis Proteins
  • Coenzymes
  • Diaminopimelic Acid
  • Pyridoxal Phosphate
  • AGD2-LIKE DEFENSE RESPONSE PROTEIN1, Arabidopsis
  • Transaminases
  • Lysine

Associated data

  • PDB/4FL0