7PUH

Crystal Structure of Two-Domain Laccase mutant H165A/R240H from Streptomyces griseoflavus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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.


Macromolecules
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
278Streptomyces griseoflavusMutation(s): 2 
EC: 1.10.3.2
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
L [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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BA [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
GA [auth D],
K [auth A],
S [auth B],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
EA [auth D]
G [auth A]
H [auth A]
CA [auth D],
DA [auth D],
EA [auth D],
G [auth A],
H [auth A],
HA [auth E],
I [auth A],
IA [auth E],
JA [auth E],
KA [auth E],
M [auth B],
N [auth B],
NA [auth F],
O [auth B],
OA [auth F],
P [auth B],
PA [auth F],
Q [auth B],
QA [auth F],
RA [auth F],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C],
MA [auth E],
T [auth B],
TA [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
OXY (Subject of Investigation/LOI)
Query on OXY

Download Ideal Coordinates CCD File 
FA [auth D]
J [auth A]
LA [auth E]
R [auth B]
SA [auth F]
FA [auth D],
J [auth A],
LA [auth E],
R [auth B],
SA [auth F],
Y [auth C]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.76α = 90
b = 94.286β = 91.273
c = 120.482γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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