5E9N

Steccherinum murashkinskyi laccase at 0.95 resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-function study of two new middle-redox potential laccases from basidiomycetes Antrodiella faginea and Steccherinum murashkinskyi.

Glazunova, O.A.Polyakov, K.M.Moiseenko, K.V.Kurzeev, S.A.Fedorova, T.V.

(2018) Int. J. Biol. Macromol. 118: 406-418

  • DOI: 10.1016/j.ijbiomac.2018.06.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Laccases are multicopper oxidases that catalyze oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. The physicochemical and catalytic properties of two new fungal laccases from basidiomycet ...

    Laccases are multicopper oxidases that catalyze oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. The physicochemical and catalytic properties of two new fungal laccases from basidiomycetes Antrodiella faginea (AfL) and Steccherinum murashkinskyi (SmL) with middle redox potential of the T1 copper site were studied. The X-ray structures of AfL and SmL were solved at 1.75 Å and 0.95 Å, respectively. The oxidized state of copper ions in the active site was observed in AfL structure, while the mixture of oxidized and reduced states was observed in SmL structure. These oxidized and reduced states relate to the position of copper ions, their coordination, and nature and position of oxygen ligands. Comparative analysis of the T1 site environment of laccases with known structure allowed us to highlight the six types of the secondary coordination sphere of the T1 copper. The solvent accessible surface area of the conservative region of the secondary coordination sphere of the T1 copper correlates with its the redox potential. It was shown that the laccase classification by the structure of the T1 copper secondary coordination sphere is in agreement to ecophysiological behavior of laccase producing fungi.


    Organizational Affiliation

    A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russian Federation. Electronic address: olga.a.glas@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Laccase 2
A
527Steccherinum murashkinskyiMutation(s): 0 
EC: 1.10.3.2
Find proteins for I1VE66 (Steccherinum murashkinskyi)
Go to UniProtKB:  I1VE66
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
PG6
Query on PG6

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Download CCD File 
A
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.510α = 90.00
b = 83.270β = 90.00
c = 111.040γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references