9NJI | pdb_00009nji

M298L Streptomyces coelicolor Laccase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.202 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Literature

Unexpected effect of an axial ligand mutation in the type 1 copper center in small laccase: structure-based analyses and engineering to increase reduction potential and activity.

Wang, J.X.Vilbert, A.C.Williams, L.H.Mirts, E.N.Cui, C.Lu, Y.

(2025) Chem Sci 

  • DOI: https://doi.org/10.1039/d5sc02177d
  • Primary Citation of Related Structures:  
    9NJI, 9NJJ

  • PubMed Abstract: 

    Type 1 copper (T1Cu) centers are crucial in biological electron transfer (ET) processes, exhibiting a wide range of reduction potentials to match their redox partners and optimize ET rates. While tuning in mononuclear T1Cu proteins like azurin has been successful, it is more difficult for multicopper oxidases. Specifically, while replacing axial methionine to leucine in azurin increased its by ∼100 mV, the corresponding M298L mutation in small laccase from Streptomyces coelicolor (SLAC) unexpectedly decreased its by 12 mV. X-ray crystallography revealed two axial water molecules in M298L-SLAC, leading to the decrease of due to decreased hydrophobicity. Structural alignment and molecular dynamics simulation indicated a key difference in T1Cu axial loop position, leading to the different outcome upon methionine to leucine mutation. Based on structural analyses, we introduced additional F195L and I200F mutations, leading to partial removal of axial waters, a 122-mV increase in , and a 7-fold increase in k cat / K M from M298L-SLAC. These findings highlight the complexity of tuning in multicopper oxidases and provide valuable insights into how structure-based protein engineering can contribute to the broader understanding of T1Cu center, and reactivity tuning for applications, such as in solar energy transfer, fuel cells, and bioremediation.


  • Organizational Affiliation

    Department of Chemistry, The University of Texas at Austin 105 East 24th Street Austin TX 78712 USA yi.lu@utexas.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper oxidase351Streptomyces coelicolorMutation(s): 1 
Gene Names: SCO6712SC4C6.22
UniProt
Find proteins for Q9XAL8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9XAL8 
Go to UniProtKB:  Q9XAL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XAL8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
I [auth A],
K [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GLY
Query on GLY

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth A],
L [auth A]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
OH (Subject of Investigation/LOI)
Query on OH

Download Ideal Coordinates CCD File 
F [auth A]HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.202 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.228α = 90
b = 177.228β = 90
c = 177.228γ = 90
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
xia2data scaling
PHENIXphasing
PHENIXrefinement
xia2data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references