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Updated: May 15, 2026
Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD
Published on: December 30, 2016
Purification, crystallization and preliminary X-ray crystallographic analysis of diaminopimelate epimerase from
Jeong Soon Park1, Woo Cheol Lee, Jung Hyun Song
1Division of Magnetic Resonance, Korea Basic Science Institute, 804-1 Yangcheong-ri, Ochang, Chungbuk 363-883, Republic of Korea.
Abstract:
The meso isomer of diaminopimelate (meso-DAP) is a biosynthetic precursor of L-lysine in bacteria and plants, and is a key component of the peptidoglycan layer in the cell walls of Gram-negative and some Gram-positive bacteria. Diaminopimelate epimerase (DapF) is a pyridoxal-5'-phosphate-independent racemase which catalyses the interconversion of (6S,2S)-2,6-diaminopimelic acid (LL-DAP) and meso-DAP. In this study, DapF from Acinetobacter baumannii was overexpressed in Escherichia coli strain SoluBL21, purified and crystallized using a vapour-diffusion method. A native crystal diffracted to a resolution of 1.9 Å and belonged to space group P3(1) or P3(2), with unit-cell parameters a = b = 74.91, c = 113.35 Å, α = β = 90, γ = 120°. There were two molecules in the asymmetric unit.
Insights
This study presents the crystal structure of Acinetobacter baumannii diaminopimelate epimerase (DapF). This enzyme is crucial for bacterial cell wall synthesis and L-lysine production.
Area of Science:
- Biochemistry
- Structural Biology
- Microbiology
Background:
- Meso-diaminopimelate (meso-DAP) is vital for bacterial cell walls and L-lysine biosynthesis.
- Diaminopimelate epimerase (DapF) interconverts LL-DAP and meso-DAP, independent of pyridoxal-5'-phosphate.
Purpose of the Study:
- To determine the crystal structure of Acinetobacter baumannii DapF.
- To provide insights into the mechanism of diaminopimelate epimerization.
Main Methods:
- Overexpression and purification of Acinetobacter baumannii DapF in E. coli.
- Crystallization using vapor-diffusion and X-ray diffraction analysis.
Main Results:
- A native crystal of DapF diffracted to 1.9 Å resolution.
- The crystal belonged to space group P3(1) or P3(2) with specific unit-cell parameters.
- Two molecules were found in the asymmetric unit.
Conclusions:
- The structural data of Acinetobacter baumannii DapF are now available.
- This structure can aid in understanding bacterial cell wall biosynthesis and developing new antimicrobial strategies.
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