6S0O

Crystal Structure of Two-Domain Laccase from Streptomyces griseoflavus produced at 0.25 mM copper sulfate in growth medium

• PDB DOI:  https://doi.org/10.2210/pdb6S0O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces griseoflavus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-17 Released: 2019-07-17 
• Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, T.V., Kolyadenko, I.A.
• Funding Organization(s): Russian Foundation for Basic Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.179 
• R-Value Work: 0.142 
• R-Value Observed: 0.142 

Literature

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

• PubMed: 31261802 
• DOI: https://doi.org/10.3390/ijms20133184
• Primary Citation of Related Structures:  
  5MKM, 6FC7, 6FDJ, 6RH9, 6RHQ, 6S0O


• PubMed Abstract: 
  

Laccases (EC 1.10.3.2) 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 .

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Organizational Affiliation: 

Institute of Protein Research RAS, Institutskaya 4, Pushchino, Moscow 142290, Russia. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 199.12 kDa 
• Atom Count: 13,409 
• Modelled Residue Count: 1,666 
• Deposited Residue Count: 1,815 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Two-domain laccase	A, D, E	322	Streptomyces griseoflavus	Mutation(s): 0  EC: 1.10.3.2
UniProt
Find proteins for A0A0M4FJ81 (Streptomyces griseoflavus) Explore A0A0M4FJ81  Go to UniProtKB:  A0A0M4FJ81

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Two-domain laccase	B, C, F	283	Streptomyces griseoflavus	Mutation(s): 0  EC: 1.10.3.2
UniProt
Find proteins for A0A0M4FJ81 (Streptomyces griseoflavus) Explore A0A0M4FJ81  Go to UniProtKB:  A0A0M4FJ81

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	DA [auth D], JA [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	CA [auth D], R [auth B], S [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	AA [auth D], BA [auth D], EA [auth E], FA [auth E], G [auth A], GA [auth E], H [auth A], HA [auth E], I [auth A], IA [auth E], J [auth A], KA [auth F], LA [auth F], M [auth B], MA [auth F], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	L [auth A], T [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
PEO	K [auth A], X [auth C]	HYDROGEN PEROXIDE H2 O2 MHAJPDPJQMAIIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.179 
• R-Value Work: 0.142 
• R-Value Observed: 0.142 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.53	α = 90
b = 94.62	β = 90.39
c = 116.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-17 
Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, T.V., Kolyadenko, I.A.

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Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	18-04-00270a

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release