Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase

EMBO J. 2003 Dec 1;22(23):6193-204. doi: 10.1093/emboj/cdg575.


Aspartate decarboxylase, which is translated as a pro-protein, undergoes intramolecular self-cleavage at Gly24-Ser25. We have determined the crystal structures of an unprocessed native precursor, in addition to Ala24 insertion, Ala26 insertion and Gly24-->Ser, His11-->Ala, Ser25-->Ala, Ser25-->Cys and Ser25-->Thr mutants. Comparative analyses of the cleavage site reveal specific conformational constraints that govern self-processing and demonstrate that considerable rearrangement must occur. We suggest that Thr57 Ogamma and a water molecule form an 'oxyanion hole' that likely stabilizes the proposed oxyoxazolidine intermediate. Thr57 and this water molecule are probable catalytic residues able to support acid-base catalysis. The conformational freedom in the loop preceding the cleavage site appears to play a determining role in the reaction. The molecular mechanism of self-processing, presented here, emphasizes the importance of stabilization of the oxyoxazolidine intermediate. Comparison of the structural features shows significant similarity to those in other self-processing systems, and suggests that models of the cleavage site of such enzymes based on Ser-->Ala or Ser-->Thr mutants alone may lead to erroneous interpretations of the mechanism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alanine
  • Amino Acid Substitution
  • Crystallography, X-Ray
  • Escherichia coli / enzymology
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism
  • Glutamate Decarboxylase / chemistry*
  • Glutamate Decarboxylase / metabolism*
  • Models, Molecular
  • Mutagenesis, Insertional
  • Mutagenesis, Site-Directed
  • Protein Processing, Post-Translational
  • Protein Structure, Secondary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism


  • Escherichia coli Proteins
  • Recombinant Proteins
  • aspartate-alpha-decarboxylase
  • Glutamate Decarboxylase
  • Alanine

Associated data

  • PDB/1PPY
  • PDB/1PQE
  • PDB/1PQF
  • PDB/1PQH
  • PDB/1PT0
  • PDB/1PT1
  • PDB/1PYQ
  • PDB/1PYU