9RC6 | pdb_00009rc6

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant Y471L co-crystallized with Copper Chloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.229 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Laccases from lactic acid bacteria show cuprous oxidase activity and capture Cu(II) and Ag(I) ions.

Gasco, R.Sendra, R.Olmeda, I.Paredes-Martinez, F.Ferrer, S.Pardo, I.Casino, P.

(2026) Protein Sci 35: e70385-e70385

  • DOI: https://doi.org/10.1002/pro.70385
  • Primary Citation of Related Structures:  
    9RC3, 9RC5, 9RC6, 9RC8, 9RCJ, 9RCK, 9RCL, 9RCM, 9RCN

  • PubMed Abstract: 

    Several laccases derived from lactic acid bacteria (LAB) display specific structural features, such as two methionine residues at the entrance of the T1Cu center, and an extended C-terminal end enriched in methionine and histidine. To investigate their functional roles, we engineered mutant variants of the laccase Pp4816 from Pediococcus pentosaceus and analyzed them using both functional and structural approaches. We identified a cuprous oxidase activity that is essential for the oxidation of 2,6-dimethoxyphenol (2,6-DMP) and other substrates, but dispensable for ABTS. The two Met residues at the entrance of the T1Cu center are crucial for this activity while the C-terminus has a minor impact and shows conformational flexibility. Through anomalous diffraction studies, we located Cu(II) bound at the entrance of the T1Cu center and additional surface sites, and demonstrated that Ag(I) acts as an inhibitor of the cuprous oxidase activity, which binds to overlapping positions, including the C-terminus. This cuprous oxidase activity was found to be conserved in other laccases from LAB, suggesting that these enzymes function as copper and silver chelators with potential biotechnological applications, such as environmental copper detoxification.


  • Organizational Affiliation
    • 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
Multicopper oxidase domain-containing proteinA,
B [auth C],
C [auth G]
532Pediococcus pentosaceusMutation(s): 4 
Gene Names: ITQ90_10235
UniProt
Find proteins for A0AB73HHR8 (Pediococcus pentosaceus)
Explore A0AB73HHR8 
Go to UniProtKB:  A0AB73HHR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AB73HHR8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
O [auth C]
P [auth C]
H [auth A],
I [auth A],
J [auth A],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
K [auth C]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
K [auth C],
L [auth C],
M [auth C],
N [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.229 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.68α = 90
b = 123.68β = 90
c = 181.77γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Generalitat ValencianaSpainCIAICO/2022/142
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2019-110630GB-I00
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2022-141621NB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references