Crystal Structure of Two-Domain Laccase mutant M199G from Streptomyces griseoflavus

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 

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Engineering the Catalytic Properties of Two-Domain Laccase from Streptomyces griseoflavus Ac-993.

Kolyadenko, I.Scherbakova, A.Kovalev, K.Gabdulkhakov, A.Tishchenko, S.

(2021) Int J Mol Sci 23

  • DOI: https://doi.org/10.3390/ijms23010065
  • Primary Citation of Related Structures:  
    7PEN, 7PES, 7PFR, 7PTM, 7PU0, 7PUH

  • PubMed Abstract: 

    Laccases catalyze the oxidation of substrates with the concomitant reduction of oxygen to water. Recently, we found that polar residues located in tunnels leading to Cu2 and Cu3 ions control oxygen entrance (His 165) and proton transport (Arg 240) of two-domain laccase (2D) from Streptomyces griseoflavus (SgfSL). In this work, we have focused on optimizing the substrate-binding pocket (SBP) of SgfSL while simultaneously adjusting the oxygen reduction process. SgfSL variants with three single (Met199Ala, Met199Gly, and Tyr230Ala) and three double amino acid residues substitutions (Met199Gly/His165Ala, His165Ala/Arg240His, Met199Gly/Arg240His) were constructed, purified, and investigated. Combination of substitutions in the SBP and in the tunnel leading to Cu2 ion (Met199Gly/Arg240His) increased SgfSL catalytic activity towards ABTS by 5-fold, and towards 2.6-DMP by 16-fold. The high activity of the Met199Gly/Arg240His variant can be explained by the combined effect of the SBP geometry optimization (Met199Gly) and increased proton flux via the tunnel leading to Cu2 ion (Arg240His). Moreover, the variant with Met199Gly and His165Ala mutations did not significantly increase SgfSL's activity, but led to a drastic shift in the optimal pH of 2.6-DMP oxidation. These results indicate that His 165 not only regulates oxygen access, but it also participates in proton transport in 2D laccases.

  • Organizational Affiliation

    Institute of Protein Research RAS, 142290 Pushchino, Russia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Two-domain laccase
A, B, C, D, E
A, B, C, D, E, F
283Streptomyces griseoflavusMutation(s): 1 
Find proteins for A0A0M4FJ81 (Streptomyces griseoflavus)
Explore A0A0M4FJ81 
Go to UniProtKB:  A0A0M4FJ81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4FJ81
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
EA [auth F]
FA [auth F]
AA [auth E],
BA [auth E],
CA [auth E],
EA [auth F],
FA [auth F],
G [auth A],
GA [auth F],
H [auth A],
HA [auth F],
I [auth A],
IA [auth F],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
T [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
OXY (Subject of Investigation/LOI)
Query on OXY

Download Ideal Coordinates CCD File 
DA [auth E],
U [auth C]
Query on NA

Download Ideal Coordinates CCD File 
JA [auth F],
K [auth A],
Q [auth B],
Z [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.175α = 90
b = 94.355β = 91.135
c = 119.795γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation19-34-90121

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description