4DZA

Crystal structure of a lysine racemase within internal aldimine linkage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants

Wu, H.M.Kuan, Y.C.Chu, C.H.Hsu, W.H.Wang, W.C.

(2012) Plos One 7: e48301-e48301

  • DOI: 10.1371/journal.pone.0048301
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lysine racemase, a pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase that catalyzes the interconversion of lysine enantiomers, is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants. Here, we ...

    Lysine racemase, a pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase that catalyzes the interconversion of lysine enantiomers, is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants. Here, we have determined the first crystal structure of a lysine racemase (Lyr) from Proteus mirabilis BCRC10725, which shows the highest activity toward lysine and weaker activity towards arginine. In addition, we establish the first broad-specificity amino acid racemase (Bar) structure from Pseudomonas putida DSM84, which presents not only the highest activity toward lysine but also remarkably broad substrate specificity. A complex structure of Bar-lysine is also established here. These structures demonstrate the similar fold of alanine racemase, which is a head-to-tail homodimer with each protomer containing an N-terminal (α/β)(8) barrel and a C-terminal β-stranded domain. The active-site residues are located at the protomer interface that is a funnel-like cavity with two catalytic bases, one from each protomer, and the PLP binding site is at the bottom of this cavity. Structural comparisons, site-directed mutagenesis, kinetic, and modeling studies identify a conserved arginine and an adjacent conserved asparagine that fix the orientation of the PLP O3 atom in both structures and assist in the enzyme activity. Furthermore, side chains of two residues in α-helix 10 have been discovered to point toward the cavity and define the substrate specificity. Our results provide a structural foundation for the design of racemases with pre-determined substrate specificity and for the development of the non-antibiotic selection system in transgenic plants.


    Organizational Affiliation

    Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
lysine racemase
A
407Proteus mirabilisMutation(s): 0 
Gene Names: lyr
EC: 5.1.1.5
Find proteins for M4GGR9 (Proteus mirabilis)
Go to UniProtKB:  M4GGR9
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 62.847α = 90.00
b = 85.086β = 90.00
c = 151.292γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHENIXphasing
MOSFLMdata reduction
PHENIXmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-01 
  • Released Date: 2013-03-06 
  • Deposition Author(s): Wang, W.C., Wu, H.M.

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release