2DU2

Crystal Structure Analysis of the L-Lactate Oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of L-lactate oxidase from Aerococcus viridans at 2.1A resolution reveals the mechanism of strict substrate recognition

Umena, Y.Yorita, K.Matsuoka, T.Kita, A.Fukui, K.Morimoto, Y.

(2006) Biochem.Biophys.Res.Commun. 350: 249-256

  • DOI: 10.1016/j.bbrc.2006.09.025

  • PubMed Abstract: 
  • L-Lactate oxidase (LOX) from Aerococcus viridans is a member of the alpha-hydroxyacid-oxidase flavoenzyme family. We have determined the three-dimensional structure of LOX and revealed the mechanism of substrate recognition. The LOX monomer structure ...

    L-Lactate oxidase (LOX) from Aerococcus viridans is a member of the alpha-hydroxyacid-oxidase flavoenzyme family. We have determined the three-dimensional structure of LOX and revealed the mechanism of substrate recognition. The LOX monomer structure has a typical alpha(8)/beta(8) motif commonly found in other flavin family proteins. A related enzyme, glycolate oxidase, catalyzes the oxidation of glycolate rather than lactate. Comparison of the two enzyme structures highlights the importance of five residues around the FMN prosthetic group of LOX, which act synergistically to discriminate between the l/d configurations of lactate. X-ray crystallography of LOX gave a space group I422 of unit-cell parameters a=b=191.096A, c=194.497A and alpha=beta=gamma=90 degrees with four monomers per asymmetric unit. The four independent monomers display slight structural differences around the active site. Diffraction data were collected, under cryogenic conditions to 2.1A resolution at the synchrotron facilities in Japan.


    Organizational Affiliation

    Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lactate oxidase
A, B, C, D
374Aerococcus viridansMutation(s): 0 
Find proteins for Q44467 (Aerococcus viridans)
Go to UniProtKB:  Q44467
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 191.096α = 90.00
b = 191.096β = 90.00
c = 194.497γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-07-19 
  • Released Date: 2006-12-05 
  • Deposition Author(s): Morimoto, Y.

Revision History 

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance