8U8R

Y229F/V290N/S292F Streptomyces coelicolor Laccase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Increasing Reduction Potentials of Type 1 Copper Center and Catalytic Efficiency of Small Laccase from Streptomyces coelicolor through Secondary Coordination Sphere Mutations.

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

(2023) Angew Chem Int Ed Engl 62: e202314019-e202314019

  • DOI: https://doi.org/10.1002/anie.202314019
  • Primary Citation of Related Structures:  
    8U8P, 8U8Q, 8U8R, 8U8S, 8U8T

  • PubMed Abstract: 

    The key to type 1 copper (T1Cu) function lies in the fine tuning of the Cu II/I reduction potential (E°' T1Cu ) to match those of its redox partners, enabling efficient electron transfer in a wide range of biological systems. While the secondary coordination sphere (SCS) effects have been used to tune E°' T1Cu in azurin over a wide range, these principles are yet to be generalized to other T1Cu-containing proteins to tune catalytic properties. To this end, we have examined the effects of Y229F, V290N and S292F mutations around the T1Cu of small laccase (SLAC) from Streptomyces coelicolor to match the high E°' T1Cu of fungal laccases. Using ultraviolet-visible absorption and electron paramagnetic resonance spectroscopies, together with X-ray crystallography and redox titrations, we have probed the influence of SCS mutations on the T1Cu and corresponding E°' T1Cu . While minimal and small E°' T1Cu increases are observed in Y229F- and S292F-SLAC, the V290N mutant exhibits a major E°' T1Cu increase. Moreover, the influence of these mutations on E°' T1Cu is additive, culminating in a triple mutant Y229F/V290N/S292F-SLAC with the highest E°' T1Cu of 556 mV vs. SHE reported to date. Further activity assays indicate that all mutants retain oxygen reduction reaction activity, and display improved catalytic efficiencies (k cat /K M ) relative to WT-SLAC.


  • Organizational Affiliation

    Department of Chemistry, The University of Texas at Austin, 105 East 24th Street, Austin, TX 78712, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper oxidase
A, B, C
351Streptomyces coelicolorMutation(s): 3 
Gene Names: SCO6712
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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
DA [auth B]
EA [auth B]
N [auth A]
O [auth A]
SA [auth C]
DA [auth B],
EA [auth B],
N [auth A],
O [auth A],
SA [auth C],
TA [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
CA [auth B],
M [auth A],
QA [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth B],
L [auth A],
RA [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GLY
Query on GLY

Download Ideal Coordinates CCD File 
AA [auth B]
FA [auth B]
H [auth A]
I [auth A]
IA [auth C]
AA [auth B],
FA [auth B],
H [auth A],
I [auth A],
IA [auth C],
J [auth A],
K [auth A],
MA [auth C],
NA [auth C],
OA [auth C],
PA [auth C],
Q [auth A],
X [auth B],
Y [auth B],
Z [auth B]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
HA [auth C]
JA [auth C]
D [auth A],
E [auth A],
F [auth A],
HA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
R [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
BO3
Query on BO3

Download Ideal Coordinates CCD File 
P [auth A]BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
OH (Subject of Investigation/LOI)
Query on OH

Download Ideal Coordinates CCD File 
G [auth A],
GA [auth C],
W [auth B]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.355α = 90
b = 177.355β = 90
c = 176.956γ = 90
Software Package:
Software NamePurpose
BOSdata collection
xia2data reduction
PHENIXphasing
PHENIXrefinement
xia2data scaling

Structure Validation

View Full Validation Report



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: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references