5LL2

Structure of Isoleucine 2-epimerase from Lactobacillus buchneri (apo form)

Summary for 5LL2

• Entry DOI: 10.2210/pdb5ll2/pdb
• Descriptor: Isoleucine 2-epimerase (2 entities in total)
• Functional Keywords: racemase, epimerase, isoleucine, plp, lactobacillus buchneri, isomerase
• Biological source: Lactobacillus buchneri
• Total number of polymer chains: 4
• Total formula weight: 211387.08

Authors

Reiser, J.-B.,Awad, R.,Gans, P. (deposition date: 2016-07-26, release date: 2017-04-12, Last modification date: 2024-05-08)

Primary citation

Awad, R.,Gans, P.,Reiser, J.B.
Structural insights into the substrate recognition and reaction specificity of the PLP-dependent fold-type I isoleucine 2-epimerase from Lactobacillus buchneri.
Biochimie, 137:165-173, 2017

PubMed Abstract: The isoleucine 2-epimerase from Lactobacillus buchneri has been previously identified and characterized to catalyze the pyridoxal 5'-phosphate (PLP)-dependent racemization and epimerization of a broad spectrum of nonpolar amino acids from L- to D-form and vice versa, in particular isoleucine. In this study, crystal structures of both native and PLP-complex forms of this racemase are presented at 2.6 and 2.15 Å resolution, respectively. Both structures show that the protein belongs to the fold-type I subgroup of PLP-dependent enzymes and is very close to aminobutyrate aminotransferases family, as it has been suspected because of their sequence homology. The extensive structural comparison with fold-type I enzymes with known amino acid racemization activities, including the α-amino-ε-caprolactam racemase from Achromobacter obae and the cystathionine β-lyase from Escherichia coli, allows us to identify the active site residues responsible for its nonpolar amino acid recognition and reactivity specificity. Our observations also suggest that the racemization reaction by the fold-type I racemases may generally occur thanks to a revised two-base mechanism. Lastly, both structures reveal details on the conformational changes provoked by PLP binding that suggest an induced fit of the active site "entrance door", necessary to accommodate PLP and substrate molecules.

PubMed: 28344038
DOI: 10.1016/j.biochi.2017.03.015

Experimental method

X-RAY DIFFRACTION (2.6 Å)