8AIP

Crystal Structure of Two-domain bacterial laccase from the actinobacterium Streptomyces carpinensis VKM Ac-1300


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Novel Two-Domain Laccase with Middle Redox Potential: Physicochemical and Structural Properties.

Trubitsina, L.I.Trubitsin, I.V.Lisov, A.V.Gabdulkhakov, A.G.Zavarzina, A.G.Belova, O.V.Larionova, A.P.Tishchenko, S.V.Leontievsky, A.A.

(2023) Biochemistry (Mosc) 88: 1658-1667

  • DOI: https://doi.org/10.1134/S0006297923100188
  • Primary Citation of Related Structures:  
    8AIP

  • PubMed Abstract: 

    The gene for a previously unexplored two-domain laccase was identified in the genome of actinobacterium Streptomyces carpinensis VKM Ac-1300. The two-domain laccase, named ScaSL, was produced in a heterologous expression system (Escherichia coli strain M15 [pREP4]). The enzyme was purified to homogeneity using affinity chromatography. ScaSL laccase, like most two-domain laccases, exhibited activity in the homotrimer form. However, unlike the most two-domain laccases, it was also active in multimeric forms. The enzyme exhibited maximum activity at 80°C and was thermally stable. Half-inactivation time of ScaSL at 80°C was 40 min. The laccase was able to oxidize a non-phenolic organic compound ABTS at a maximum rate at pH 4.7, and to oxidized a phenolic compound 2,6-dimethoxyphenol at a maximum rate at pH 7.5. The laccase stability was observed in the pH range 9-11. At pH 7.5, laccase was slightly inhibited by sodium azide, sodium fluoride, and sodium chloride; at pH 4.5, the laccase was completely inhibited by 100 mM sodium azide. The determined K m and k cat of the enzyme for ABTS were 0.1 mM and 20 s -1 , respectively. The K m and k cat for 2,6-dimethoxyphenol were 0.84 mM and 0.36 s -1 , respectively. ScaSL catalyzed polymerization of humic acids and lignin. Redox potential of the laccase was 0.472 ± 0.007 V. Thus, the ScaSL laccase is the first characterized two-domain laccase with a middle redox potential. Crystal structure of ScaSL was determined with 2.35 Å resolution. Comparative analysis of the structures of ScaSL and other two-domain laccases suggested that the middle potential of ScaSL may be associated with conformational differences in the position of the side groups of amino acids at position 230 (in ScaSL numbering), which belong to the second coordination sphere of the copper atom of the T1 center.


  • Organizational Affiliation

    Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. lyubov_yurevich@mail.ru.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Two-Domain Laccase293Streptomyces carpinensisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.962α = 90
b = 97.962β = 90
c = 97.962γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Federation President GrantRussian Federation--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Database references