5WYF

Structure of amino acid racemase, 2.12 A

• PDB DOI:  https://doi.org/10.2210/pdb5WYF/pdb

• Classification: ISOMERASE
• Organism(s): Lentilactobacillus buchneri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-12 Released: 2017-04-19 
• Deposition Author(s): Sakuraba, H., Mutaguchi, Y., Hayashi, J., Ohshima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.221 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

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

Hayashi, J., Mutaguchi, Y., Minemura, Y., Nakagawa, N., Yoneda, K., Ohmori, T., Ohshima, T., Sakuraba, H.

(2017) Acta Crystallogr D Struct Biol 73: 428-437

• PubMed: 28471367 
• DOI: https://doi.org/10.1107/S2059798317005332
• Primary Citation of Related Structures:  
  4YSN, 4YSV, 5WYA, 5WYF


• 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.

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Organizational Affiliation: 

Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 208.33 kDa 
• Atom Count: 14,327 
• Modelled Residue Count: 1,780 
• Deposited Residue Count: 1,848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoleucine 2-epimerase	A, B, C, D	462	Lentilactobacillus buchneri	Mutation(s): 0  EC: 5.1.1.21
UniProt
Find proteins for M1GRN3 (Lentilactobacillus buchneri) Explore M1GRN3  Go to UniProtKB:  M1GRN3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ILP	E [auth A], JA [auth D], P [auth B], Y [auth C]	N-[O-PHOSPHONO-PYRIDOXYL]-ISOLEUCINE C14 H23 N2 O7 P GZZDWFDWHXPWJK-QPUJVOFHSA-N
CD	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], PA [auth D], Q [auth B], QA [auth D], R [auth B], RA [auth D], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Z [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.221 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.514	α = 90
b = 85.277	β = 96.93
c = 186.566	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Sakuraba, H., Mutaguchi, Y., Hayashi, J., Ohshima, T.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-05-17
  Changes: Database references