Crystal Structure of Two-Domain Laccase mutant H165A from Streptomyces griseoflavus with high copper ions occupancy

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase fromStreptomyces griseoflavusAc-993.

Gabdulkhakov, A.Kolyadenko, I.Kostareva, O.Mikhaylina, A.Oliveira, P.Tamagnini, P.Lisov, A.Tishchenko, S.

(2019) Int J Mol Sci 20

  • DOI: https://doi.org/10.3390/ijms20133184
  • Primary Citation of Related Structures:  
    5MKM, 6FC7, 6FDJ, 6RH9, 6RHQ, 6S0O

  • PubMed Abstract: 

    Laccases (EC are multicopper oxidoreductases acting on diphenols and related substances. Laccases are highly important for biotechnology and environmental remediation. These enzymes contain mononuclear one T2 copper ion and two T3 copper ions (Cu3 α and Cu3 β ), which form the so-called trinuclear center (TNC). Along with the typical three-domain laccases Bacteria produce two-domain (2D) enzymes, which are active at neutral and basic pH, thermostable, and resistant to inhibitors. In this work we present the comparative analysis of crystal structures and catalytic properties of recombinant 2D laccase from Streptomyces griseoflavus Ac-993 (SgfSL) and its four mutant forms with replacements of two amino acid residues, located at the narrowing of the presumable T3-solvent tunnels. We obtained inactive enzymes with substitutions of His165, with Phe, and Ile170 with Ala or Phe. His165Ala variant was more active than the wild type. We suggest that His165 is a "gateway" at the O 2 -tunnel leading from solvent to the Cu3 β of the enzyme. The side chain of Ile170 could be indirectly involved in the coordination of copper ions at the T3 center by maintaining the position of the imidazole ring of His157 that belongs to the first coordination sphere of Cu3 α .

  • Organizational Affiliation

    Institute of Protein Research RAS, Institutskaya 4, Pushchino, Moscow 142290, 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, G, H, I, J, K, L
322Streptomyces 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
Query on GOL

Download Ideal Coordinates CCD File 
DB [auth H]
GA [auth D]
HB [auth I]
MA [auth E]
NA [auth E]
DB [auth H],
GA [auth D],
HB [auth I],
MA [auth E],
NA [auth E],
NB [auth J],
OB [auth J],
R [auth A],
RA [auth F],
UB [auth K],
WA [auth G],
ZB [auth L]
C3 H8 O3
Query on CU

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth G]
BA [auth D]
BB [auth H]
CA [auth D]
AA [auth C],
AB [auth G],
BA [auth D],
BB [auth H],
CA [auth D],
CB [auth H],
DA [auth D],
EA [auth D],
EB [auth H],
FA [auth D],
FB [auth H],
GB [auth I],
IA [auth D],
IB [auth J],
JA [auth D],
JB [auth J],
KA [auth E],
KB [auth J],
LA [auth E],
LB [auth J],
M [auth A],
MB [auth J],
N [auth A],
O [auth A],
OA [auth E],
P [auth A],
PA [auth E],
PB [auth J],
Q [auth A],
QA [auth F],
RB [auth J],
SA [auth G],
SB [auth K],
T [auth A],
TA [auth G],
TB [auth K],
U [auth A],
UA [auth G],
V [auth B],
VA [auth G],
W [auth B],
WB [auth K],
XB [auth K],
Y [auth B],
YA [auth G],
YB [auth L],
Z [auth B],
ZA [auth G]
Query on OXY

Download Ideal Coordinates CCD File 
HA [auth D]
QB [auth J]
S [auth A]
VB [auth K]
X [auth B]
HA [auth D],
QB [auth J],
S [auth A],
VB [auth K],
X [auth B],
XA [auth G]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.369α = 90.13
b = 95.118β = 90.11
c = 116.475γ = 91.85
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation--

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description