Crystal Structure of d‑Ornithine/d‑Lysine Decarboxylase, a Stereoinverting Decarboxylase:
Implications for Substrate Specificity and Stereospecificity of Fold
III Decarboxylases
posted on 2019-01-30, 00:00authored byRobert S. Phillips, Pafe Poteh, Donovan Krajcovic, Katherine A. Miller, Timothy R. Hoover
A newly
discovered Fold III pyridoxal 5′-phosphate (PLP)-dependent
decarboxylase, d-ornithine/lysine decarboxylase (DOKDC),
catalyzes decarboxylation of d-lysine and d-ornithine
with inversion of stereochemistry. The X-ray crystal structure of
DOKDC has been determined to 1.72 Å. DOKDC has a low level of
sequence identity (<30%) with meso-diaminopimelate
decarboxylase (DAPDC) and l-lysine/ornithine decarboxylase
(LODC), but its three-dimensional structure is very similar. The distal
binding site of DAPDC contains a conserved arginine that forms an
ion pair with the l-carboxylate end of DAP. In both LODC
and DOKDC, this distal site is modified by replacement of the arginine
with aspartate, changing the substrate specificity. l-Ornithine
decarboxylase (ODC) and LODC have a conserved phenylalanine on the re-face of the PLP complex that has been found to play a
key role in the decarboxylation mechanism. We have found that both
DAPDC and DOKDC have tyrosine instead of phenylalanine at this position,
which precludes the binding of l-amino acids. Because the
PLP-binding lysine in ODC, LODC, DAPDC, and DOKDC is located on the re-face of the PLP, we propose that this is the acid group
responsible for protonation of the product, thus resulting in the
observed retention of configuration for decarboxylation of l-amino acids and inversion for decarboxylation of d-amino
acids. The reactions of DAPDC and DOKDC are likely accelerated by
positive electrostatics on the re-face by the lysine
ε-ammonium ion and on the si-face by closure
of the lid over the active site, resulting in desolvation and destabilization
of the d-amino acid carboxylate.