PDBsum entry 5ll3

Isomerase

PDB id: 5ll3

Contents

Protein chains

417 a.a.

Ligands

PLP ×4

Waters ×780

PDB id:

5ll3

Name:

Isomerase

Title:

Structure of the isoleucine 2-epimerase from lactobacillus buchneri (plp complex form)

Structure:

Isoleucine 2-epimerase. Chain: a, b, c, d. Synonym: bcaa racemase. Engineered: yes

Source:

Lactobacillus buchneri. Organism_taxid: 1581. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.15Å R-factor: 0.179 R-free: 0.218

Authors:

J.-B.Reiser,R.Awad,P.Gans

Key ref:

R.Awad et al. (2017). 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. PubMed id: 28344038 DOI: 10.1016/j.biochi.2017.03.015

Date:

26-Jul-16 Release date: 12-Apr-17

Protein chains

M1GRN3  (ILE2E_LENBU) -  Isoleucine 2-epimerase from Lentilactobacillus buchneri

Seq: 450 a.a.

Struc: 417 a.a.

Enzyme reactions

• Enzyme class: E.C.5.1.1.21 - isoleucine 2-epimerase.
• Reaction: L-isoleucine = D-allo-isoleucine
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.biochi.2017.03.015

Biochimie 137:165-173 (2017)

PubMed id: 28344038

Structural insights into the substrate recognition and reaction specificity of the PLP-dependent fold-type I isoleucine 2-epimerase from Lactobacillus buchneri.

R.Awad, P.Gans, J.B.Reiser.

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.