8UFY | pdb_00008ufy

High Resolution structure of A. viridans Lactate Oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.162 (Depositor), 0.156 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8UFY

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

An engineered lactate oxidase based electrochemical sensor for continuous detection of biomarker lactic acid in human sweat and serum.

He, Q.Wang, C.Jain, R.Byrnes, J.Farquhar, E.R.Reed, E.Berezovsky, E.Chance, M.R.Lodowski, D.An, R.

(2024) Heliyon 10: e34301-e34301

  • DOI: https://doi.org/10.1016/j.heliyon.2024.e34301
  • Primary Citation Related Structures: 
    8UFY

  • PubMed Abstract: 

    Lactate levels in humans reveal intensity and duration of exertion and provide a critical readout for the severity of life-threatening illnesses such as pediatric sepsis. Using the lactate oxidase enzyme (Lox) from Aerococcus viridians , we demonstrated its functionality for lactate electrochemical sensing in physiological fluids in a lab setting. The structure and dynamics of LOx were validated by crystallography, X-ray scattering, and hydroxyl radical protein footprinting. This provided a validated protein template for understanding and designing an enzyme-based electrochemical sensing elements. Using this template, LOx enzyme variants were generated and compared. Comparison of the variants demonstrates that one exhibits effective lactate sensing at significantly reduced operating voltages. Additionally, we demonstrate that the four hexahistidine-tags on each enzyme tetramer are sufficient for immobilization to create a durable, functional sensor, with no need for a covalent attachment, enabling self-immobilization and eliminating the need for additional immobilization steps. The functionality of the LOx enzyme variants was verified at physiological lactate concentrations in both human serum (0-4 mM) and artificial sweat (0-100 mM) using 3-electrode setups for analysis of the three variants in parallel. Accuracy of measurement in both artificial sweat and human serum were high. Employing a microfluidic flow cell, we successfully monitored varying lactate levels in physiological fluids continuously over a 2h period. Overall, this optimized LOx enzyme, which self-immobilizes onto gold sensing electrodes, facilitates efficient and reliable lactate detection and continuous monitoring at reduced operating voltages suitable for further development towards commercial use.


  • Organizational Affiliation
    • Department of Biomedical Engineering, University of Houston, United States.

Macromolecule Content 

  • Total Structure Weight: 84.87 kDa 
  • Atom Count: 6,401 
  • Modeled Residue Count: 705 
  • Deposited Residue Count: 760 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-lactate oxidase
A, B
380Aerococcus viridansMutation(s): 0 
EC: 1.1.3
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ44467
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
(Subject of Investigation/LOI)

Query on FMN



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
LAC
(Subject of Investigation/LOI)

Query on LAC



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
PYR
(Subject of Investigation/LOI)

Query on PYR



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B]
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.162 (Depositor), 0.156 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.262α = 90
b = 132.262β = 90
c = 91.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesNB18-20-24

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Database references