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Crystal structure of the novel amino‐acid racemase isoleucine 2‐epimerase from Lactobacillus buchneri

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′‐ph...

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Published in:Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2017-05, Vol.73 (5), p.428-437
Main Authors: Hayashi, Junji, Mutaguchi, Yuta, Minemura, Yume, Nakagawa, Noriko, Yoneda, Kazunari, Ohmori, Taketo, Ohshima, Toshihisa, Sakuraba, Haruhiko
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cited_by cdi_FETCH-LOGICAL-c3460-7f6e1c3c85a54dc90fa9ce4f8559523edeebebb68ce6917fc75ecc658e89dae3
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container_title Acta crystallographica. Section D, Biological crystallography.
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creator Hayashi, Junji
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description 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‐ϵ‐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 ion 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. Structural analysis of an isoleucine 2‐epimerase from L. buchneri provided new insight into the catalytic mechanism of bacterial fold‐type I racemases.
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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 ion 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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Section D, Biological crystallography.</jtitle><addtitle>Acta Crystallogr D Struct Biol</addtitle><date>2017-05</date><risdate>2017</risdate><volume>73</volume><issue>5</issue><spage>428</spage><epage>437</epage><pages>428-437</pages><issn>2059-7983</issn><issn>0907-4449</issn><eissn>2059-7983</eissn><eissn>1399-0047</eissn><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‐ϵ‐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 ion 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. Structural analysis of an isoleucine 2‐epimerase from L. buchneri provided new insight into the catalytic mechanism of bacterial fold‐type I racemases.</abstract><cop>5 Abbey Square, Chester, Cheshire CH1 2HU, England</cop><pub>International Union of Crystallography</pub><pmid>28471367</pmid><doi>10.1107/S2059798317005332</doi><tpages>9</tpages></addata></record>
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identifier ISSN: 2059-7983
ispartof Acta crystallographica. Section D, Biological crystallography., 2017-05, Vol.73 (5), p.428-437
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source Wiley-Blackwell Read & Publish Collection; Alma/SFX Local Collection
subjects 4-Aminobutyrate transaminase
Amino Acid Isomerases - chemistry
Amino Acid Isomerases - metabolism
Amino Acid Sequence
Amino acids
Amino-acid racemase
Binding
Caprolactam
Chain branching
Crystal structure
Crystallography, X-Ray
d‐amino acids
E coli
Enzymes
Epimerase
Hydrogen
Isoleucine
Isoleucine - analogs & derivatives
Isoleucine - chemistry
Isoleucine - metabolism
isoleucine 2‐epimerase
Lactobacillus - chemistry
Lactobacillus - enzymology
Lactobacillus - metabolism
Lactobacillus buchneri
Models, Molecular
Protein Conformation
pyridoxal 5′‐phosphate
Pyridoxal Phosphate - analogs & derivatives
Pyridoxal Phosphate - metabolism
Residues
Sequence Alignment
Site-directed mutagenesis
Solvents
title Crystal structure of the novel amino‐acid racemase isoleucine 2‐epimerase from Lactobacillus buchneri
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