5WYA

Structure of amino acid racemase, 2.65 A

Summary for 5WYA

• Entry DOI: 10.2210/pdb5wya/pdb
• Related: 5WYF
• Descriptor: Isoleucine 2-epimerase, (2S,3S)-3-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanoic acid, DIMETHYL SULFOXIDE, ... (4 entities in total)
• Functional Keywords: fold type i, plp-dependent enzyme, isomerase
• Biological source: Lactobacillus buchneri
• Total number of polymer chains: 4
• Total formula weight: 200237.57

Authors

Sakuraba, H.,Mutaguchi, Y.,Hayashi, J.,Ohshima, T. (deposition date: 2017-01-11, release date: 2017-04-19, Last modification date: 2024-03-20)

Primary citation

Hayashi, J.,Mutaguchi, Y.,Minemura, Y.,Nakagawa, N.,Yoneda, K.,Ohmori, T.,Ohshima, T.,Sakuraba, H.
Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri.
Acta Crystallogr D Struct Biol, 73:428-437, 2017

PubMed Abstract: Crystal structures of Lactobacillus buchneri isoleucine 2-epimerase, a novel branched-chain amino-acid racemase, were determined for the enzyme in the apo form, in complex with pyridoxal 5'-phosphate (PLP), in complex with N-(5'-phosphopyridoxyl)-L-isoleucine (PLP-L-Ile) and in complex with N-(5'-phosphopyridoxyl)-D-allo-isoleucine (PLP-D-allo-Ile) at resolutions of 2.77, 1.94, 2.65 and 2.12 Å, respectively. The enzyme assembled as a tetramer, with each subunit being composed of N-terminal, C-terminal and large PLP-binding domains. The active-site cavity in the apo structure was much more solvent-accessible than that in the PLP-bound structure. This indicates that a marked structural change occurs around the active site upon binding of PLP that provides a solvent-inaccessible environment for the enzymatic reaction. The main-chain coordinates of the L. buchneri isoleucine 2-epimerase monomer showed a notable similarity to those of α-amino-ℇ-caprolactam racemase from Achromobactor obae and γ-aminobutyrate aminotransferase from Escherichia coli. However, the amino-acid residues involved in substrate binding in those two enzymes are only partially conserved in L. buchneri isoleucine 2-epimerase, which may account for the differences in substrate recognition by the three enzymes. The structures bound with reaction-intermediate analogues (PLP-L-Ile and PLP-D-allo-Ile) and site-directed mutagenesis suggest that L-isoleucine epimerization proceeds through abstraction of the α-hydrogen of the substrate by Lys280, while Asp222 serves as the catalytic residue adding an α-hydrogen to the quinonoid intermediate to form D-allo-isoleucine.

PubMed: 28471367
DOI: 10.1107/S2059798317005332

Experimental method

X-RAY DIFFRACTION (2.65 Å)