2J6X

The crystal structure of lactate oxidase

• PDB DOI: https://doi.org/10.2210/pdb2J6X/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aerococcus viridans
• Mutation(s): No 


• Deposited: 2006-10-05 Released: 2006-10-23 
• Deposition Author(s): Leiros, I., Wang, E., Rasmussen, T., Oksanen, E., Repo, H., Petersen, S.B., Heikinheimo, P., Hough, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

The 2.1 A Structure of Aerococcus Viridans L-Lactate Oxidase (Lox).

Leiros, I., Wang, E., Rasmussen, T., Oksanen, E., Repo, H., Petersen, S.B., Heikinheimo, P., Hough, E.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 1185

• PubMed: 17142893 
• DOI: https://doi.org/10.1107/S1744309106044678
• Primary Citation of Related Structures:  
  2J6X


• PubMed Abstract: 
  

  The crystal structure of L-lactate oxidase (LOX) from Aerococcus viridans has been determined at 2.1 A resolution. LOX catalyzes the flavin mononucleotide (FMN) dependent oxidation of lactate to pyruvate and hydrogen peroxide. LOX belongs to the alpha-hydroxy-acid oxidase flavoenzyme family; members of which bind similar substrates and to some extent have conserved catalytic properties and structural motifs. LOX crystallized as two tightly packed tetramers in the asymmetric unit, each having fourfold symmetry. The present structure shows a conserved FMN coordination, but also reveals novel residues involved in substrate binding compared with other family members.

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Organizational Affiliation: 

NorStruct, University of Tromsø, N-9037 Tromsø, Norway.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 330.99 kDa 
• Atom Count: 23,895 
• Modelled Residue Count: 2,897 
• Deposited Residue Count: 2,992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LACTATE OXIDASE	A, B, C, D, E, F, G, H	374	Aerococcus viridans	Mutation(s): 0  EC: 1.1.3.2 (PDB Primary Data), 1.1.3 (UniProt)
UniProt
Find proteins for Q44467 (Aerococcus viridans (strain ATCC 11563 / DSM 20340 / CCUG 4311 / JCM 20461 / NBRC 12219 / NCTC 8251 / M1)) Explore Q44467  Go to UniProtKB:  Q44467

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	I [auth A], J [auth B], K [auth C], L [auth D], N [auth E], O [auth F], P [auth G], Q [auth H]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
ZN	M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.34	α = 90
b = 134.74	β = 90
c = 185.56	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-23 
Deposition Author(s): Leiros, I., Wang, E., Rasmussen, T., Oksanen, E., Repo, H., Petersen, S.B., Heikinheimo, P., Hough, E.

Revision History  

• Version 1.0: 2006-10-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description