5FAG
Alanine Racemase from Streptomyces coelicolor A3(2) with Bound Propionate Inhibitor
Summary for 5FAG
| Entry DOI | 10.2210/pdb5fag/pdb |
| Descriptor | Alanine racemase, PYRIDOXAL-5'-PHOSPHATE, PROPANOIC ACID, ... (6 entities in total) |
| Functional Keywords | isomerase, plp, alanine racemase, propionate |
| Biological source | Streptomyces coelicolor A3(2) |
| Total number of polymer chains | 4 |
| Total formula weight | 175315.92 |
| Authors | Tassoni, R.,Pannu, N.S. (deposition date: 2015-12-11, release date: 2016-12-21, Last modification date: 2024-01-10) |
| Primary citation | Tassoni, R.,van der Aart, L.T.,Ubbink, M.,van Wezel, G.P.,Pannu, N.S. Structural and functional characterization of the alanine racemase from Streptomyces coelicolor A3(2). Biochem. Biophys. Res. Commun., 483:122-128, 2017 Cited by PubMed Abstract: The conversion of l-alanine (L-Ala) into d-alanine (D-Ala) in bacteria is performed by pyridoxal phosphate-dependent enzymes called alanine racemases. D-Ala is an essential component of the bacterial peptidoglycan and hence required for survival. The Gram-positive bacterium Streptomyces coelicolor has at least one alanine racemase encoded by alr. Here, we describe an alr deletion mutant of S. coelicolor which depends on D-Ala for growth and shows increased sensitivity to the antibiotic d-cycloserine (DCS). The crystal structure of the alanine racemase (Alr) was solved with and without the inhibitors DCS or propionate, at 1.64 Å and 1.51 Å resolution, respectively. The crystal structures revealed that Alr is a homodimer with residues from both monomers contributing to the active site. The dimeric state of the enzyme in solution was confirmed by gel filtration chromatography, with and without L-Ala or d-cycloserine. The activity of the enzyme was 66 ± 3 U mg for the racemization of L- to D-Ala, and 104 ± 7 U mg for the opposite direction. Comparison of Alr from S. coelicolor with orthologous enzymes from other bacteria, including the closely related d-cycloserine-resistant Alr from S. lavendulae, strongly suggests that structural features such as the hinge angle or the surface area between the monomers do not contribute to d-cycloserine resistance, and the molecular basis for resistance therefore remains elusive. PubMed: 28042035DOI: 10.1016/j.bbrc.2016.12.183 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.51 Å) |
Structure validation
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