RRC ID |
50845
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Author |
Hayashi J, Mutaguchi Y, Minemura Y, Nakagawa N, Yoneda K, Ohmori T, Ohshima T, Sakuraba H.
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Title |
Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri.
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Journal |
Acta Crystallogr D Struct Biol
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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.
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Volume |
73(Pt 5)
|
Pages |
428-437
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Published |
2017-5-1
|
DOI |
10.1107/S2059798317005332
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PII |
S2059798317005332
|
PMID |
28471367
|
MeSH |
Amino Acid Isomerases / chemistry*
Amino Acid Isomerases / metabolism*
Amino Acid Sequence
Crystallography, X-Ray
Isoleucine / analogs & derivatives
Isoleucine / chemistry
Isoleucine / metabolism*
Lactobacillus / chemistry
Lactobacillus / enzymology*
Lactobacillus / metabolism
Models, Molecular
Protein Conformation
Pyridoxal Phosphate / analogs & derivatives
Pyridoxal Phosphate / metabolism
Sequence Alignment
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IF |
3.099
|
Times Cited |
6
|
Resource |
General Microbes |
JCM 1115 |