6XIZ

Crystal structure of multi-copper oxidase from Pediococcus acidilactici


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.116 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis and biochemical properties of laccase enzymes from two Pediococcus species.

Olmeda, I.Casino, P.Collins, R.E.Sendra, R.Callejon, S.Huesa, J.Soares, A.S.Ferrer, S.Pardo, I.

(2021) Microb Biotechnol 14: 1026-1043

  • DOI: https://doi.org/10.1111/1751-7915.13751
  • Primary Citation of Related Structures:  
    6XIZ, 6XJ0, 6Z0J, 6Z0K

  • PubMed Abstract: 

    Prokaryotic laccases are emergent biocatalysts. However, they have not been broadly found and characterized in bacterial organisms, especially in lactic acid bacteria. Recently, a prokaryotic laccase from the lactic acid bacterium Pediococcus acidilactici 5930, which can degrade biogenic amines, was discovered. Thus, our study aimed to shed light on laccases from lactic acid bacteria focusing on two Pediococcus laccases, P. acidilactici 5930 and Pediococcus pentosaceus 4816, which have provided valuable information on their biochemical activities on redox mediators and biogenic amines. Both laccases are able to oxidize canonical substrates as ABTS, ferrocyanide and 2,6-DMP, and non-conventional substrates as biogenic amines. With ABTS as a substrate, they prefer an acidic environment and show sigmoidal kinetic activity, and are rather thermostable. Moreover, this study has provided the first structural view of two lactic acid bacteria laccases, revealing new structural features not seen before in other well-studied laccases, but which seem characteristic for this group of bacteria. We believe that understanding the role of laccases in lactic acid bacteria will have an impact on their biotechnological applications and provide a framework for the development of engineered lactic acid bacteria with enhanced properties.


  • Organizational Affiliation

    ENOLAB, Institut de Biotecnologia i Biomedicina (BioTecMed), Universitat de València, Valencia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper oxidase
A, B
477Pediococcus acidilacticiMutation(s): 0 
Gene Names: BTW26_06860FEZ49_06610
UniProt
Find proteins for A0A1A5VCP7 (Pediococcus acidilactici)
Explore A0A1A5VCP7 
Go to UniProtKB:  A0A1A5VCP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1A5VCP7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2O (Subject of Investigation/LOI)
Query on C2O

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
CU-O-CU LINKAGE
Cu2 O
BERDEBHAJNAUOM-UHFFFAOYSA-N
BEN
Query on BEN

Download Ideal Coordinates CCD File 
J [auth B]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
C [auth A],
E [auth A],
G [auth B],
I [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.116 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.06α = 90
b = 147.3β = 98.55
c = 65.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM111244
Department of Energy (DOE, United States)United StatesKP1605010
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R21GM129570-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1P30GM133893
Department of Energy (DOE, United States)United StatesBER- BO 070
Department of Energy (DOE, United States)United StatesBES-FWP-PS001

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references