Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase

Protein Sci. 2008 Dec;17(12):2080-90. doi: 10.1110/ps.037440.108. Epub 2008 Sep 11.


In recent years, dihydrodipicolinate synthase (DHDPS, E.C. has received considerable attention from a mechanistic and structural viewpoint. DHDPS catalyzes the reaction of (S)-aspartate-beta-semialdehyde with pyruvate, which is bound via a Schiff base to a conserved active-site lysine (Lys161 in the enzyme from Escherichia coli). To probe the mechanism of DHDPS, we have studied the inhibition of E. coli DHDPS by the substrate analog, beta-hydroxypyruvate. The K (i) was determined to be 0.21 (+/-0.02) mM, similar to that of the allosteric inhibitor, (S)-lysine, and beta-hydroxypyruvate was observed to cause time-dependent inhibition. The inhibitory reaction with beta-hydroxypyruvate could be qualitatively followed by mass spectrometry, which showed initial noncovalent adduct formation, followed by the slow formation of the covalent adduct. It is unclear whether beta-hydroxypyruvate plays a role in regulating the biosynthesis of meso-diaminopimelate and (S)-lysine in E. coli, although we note that it is present in vivo. The crystal structure of DHDPS complexed with beta-hydroxypyruvate was solved. The active site clearly showed the presence of the inhibitor covalently bound to the Lys161. Interestingly, the hydroxyl group of beta-hydroxypyruvate was hydrogen-bonded to the main-chain carbonyl of Ile203. This provides insight into the possible catalytic role played by this peptide unit, which has a highly strained torsion angle (omega approximately 201 degrees ). A survey of the known DHDPS structures from other organisms shows this distortion to be a highly conserved feature of the DHDPS active site, and we propose that this peptide unit plays a critical role in catalysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biocatalysis
  • Catalytic Domain
  • Crystallography, X-Ray
  • Escherichia coli / enzymology
  • Hydro-Lyases / antagonists & inhibitors
  • Hydro-Lyases / chemistry*
  • Hydro-Lyases / metabolism*
  • Isoleucine / chemistry
  • Isoleucine / metabolism*
  • Kinetics
  • Lysine / biosynthesis
  • Lysine / metabolism*
  • Models, Molecular
  • Peptides / chemistry
  • Protein Conformation
  • Pyruvates / chemistry
  • Pyruvates / metabolism
  • Pyruvates / pharmacology
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Structure-Activity Relationship
  • Thermotoga maritima / enzymology


  • Peptides
  • Pyruvates
  • Isoleucine
  • hydroxypyruvic acid
  • Hydro-Lyases
  • 4-hydroxy-tetrahydrodipicolinate synthase
  • Lysine