Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase

Bindu Pillai, Maia Cherney, Christopher M. Diaper, Andrew Sutherland, John S. Blanchard, John C. Vederas, Michael N G James

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Diaminopimelate (DAP) epimerase catalyzes the stereoinversion of ll-DAP to meso-DAP, a precursor of l-lysine and an essential component of the bacterial peptidoglycan. This function is vital to bacteria and the enzyme therefore represents an attractive target for the design of novel anti-bacterials. DAP epimerase belongs to the group of PLP-independent amino acid racemases that function through a rather unusual mechanism involving two cysteines acting in concert as a base (thiolate) and an acid (thiol). We have solved the crystal structures of the apo-forms of DAP epimerase mutants (C73S and C217S) from Haemophilus influenzae at 2.3 Å and 2.2 Å resolution, respectively. These structures provide a snapshot of the enzyme in the first step of the catalytic cycle. Comparisons with the structures of the inhibitor-bound form reveal that the enzyme adopts an 'open conformation' in the absence of substrates or inhibitors with the two active site cysteines existing as a thiol-thiolate pair. Substrate binding to the C-terminal domain triggers the closure of the N-terminal domain coupled with tight encapsulation of the ligand, stabilization of the conformation of an active site loop containing Cys73 and expulsion of water molecules with concomitant desolvation of the thiolate base. This structural rearrangement is critical for catalysis.

Original languageEnglish (US)
Pages (from-to)547-553
Number of pages7
JournalBiochemical and Biophysical Research Communications
Volume363
Issue number3
DOIs
StatePublished - Nov 23 2007

Fingerprint

diaminopimelate epimerase
Catalysis
Crystal structure
Sulfhydryl Compounds
Amino Acid Isomerases
Cysteine
Conformations
Catalytic Domain
Enzymes
Peptidoglycan
Haemophilus influenzae
Substrates
Encapsulation
Lysine
Bacteria
Stabilization
Ligands
Molecules
Acids
Water

Keywords

  • Active site mutants
  • Catalytic mechanism
  • Crystal structure
  • DAP epimerase
  • Domain closure

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

Cite this

Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase. / Pillai, Bindu; Cherney, Maia; Diaper, Christopher M.; Sutherland, Andrew; Blanchard, John S.; Vederas, John C.; James, Michael N G.

In: Biochemical and Biophysical Research Communications, Vol. 363, No. 3, 23.11.2007, p. 547-553.

Research output: Contribution to journalArticle

Pillai, Bindu ; Cherney, Maia ; Diaper, Christopher M. ; Sutherland, Andrew ; Blanchard, John S. ; Vederas, John C. ; James, Michael N G. / Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase. In: Biochemical and Biophysical Research Communications. 2007 ; Vol. 363, No. 3. pp. 547-553.
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