posted on 2024-01-08, 13:07authored byEmma H. Kelley, George Minasov, Katherine Konczak, Ludmilla Shuvalova, Joseph S. Brunzelle, Shantanu Shukla, Megan Beulke, Teerana Thabthimthong, Kenneth W. Olsen, Nicole L. Inniss, Karla J. F. Satchell, Daniel P. Becker
There is an urgent need for new antibiotics given the
rise of antibiotic
resistance, and succinyl-diaminopimelate desuccinylase (DapE, E.C.
3.5.1.18) has emerged as a promising bacterial enzyme target. DapE
from Haemophilus influenzae (HiDapE) has been studied and inhibitors identified, but
it is essential to explore DapE from different species to assess selective
versus broad-spectrum therapeutics. We have determined the structure
of DapE from the ESKAPE pathogen Acinetobacter baumannii (AbDapE) and studied inhibition by known inhibitors
of HiDapE. AbDapE is inhibited by
captopril and sulfate comparable to HiDapE, but AbDapE was not significantly inhibited by a known indoline
sulfonamide HiDapE inhibitor. Captopril and sulfate
both stabilize HiDapE by increasing the thermal melting
temperature (Tm) in thermal shift assays.
By contrast, sulfate decreases the stability of the AbDapE enzyme, whereas captopril increases the stability. Further,
we report two crystal structures of selenomethionine-substituted AbDapE in the closed conformation, one with AbDapE in complex with succinate derived from enzymatic hydrolysis
of N6-methyl-l,l-SDAP
substrate and acetate (PDB code 7T1Q, 2.25 Å resolution), and a crystal
structure of AbDapE with bound succinate along with l-(S)-lactate, a product of degradation of citric acid from
the crystallization buffer during X-ray irradiation (PDB code 8F8O, 2.10 Å resolution).