6YZF | pdb_00006yzf

Crystal structure of the M295Y variant of Ssl1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.232 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.200 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Substitution of the axial Type 1 Cu Ligand Afford Binding of a Water Molecule in Axial Position Affecting Kinetics, Spectral, and Structural Properties of the Small Laccase Ssl1.

Olbrich, A.C.Mielenbrink, S.Willers, V.P.Koschorreck, K.Birrell, J.A.Span, I.Urlacher, V.B.

(2024) Chemistry : e202403005-e202403005

  • DOI: https://doi.org/10.1002/chem.202403005
  • Primary Citation of Related Structures:  
    6Y4A, 6YO5, 6YZD, 6YZF, 6YZY

  • PubMed Abstract: 

    Multicopper oxidases use Cu ions as cofactors to oxidize various substrates. High reduction potential at Type 1 Cu is considered as crucial for effective catalysis. Previous studies have shown that replacing the axial methionine ligand of the Type 1 Cu with leucine or phenylalanine leads to an increased reduction potential, but not always to higher enzyme activity. Here we present a study on six variants of the small laccase Ssl1 from Streptomyces sviceus, where the axial methionine ligand was substituted, and the effect of the axial ligand on reduction potential, activity, spectral properties and structure was investigated. Absorption, electronic circular dichroism and EPR spectra revealed the presence of a stronger coordinating axial ligand like oxygen, which influences the electronic and catalytic properties more than the nature of the amino acid side chain. The crystal structures of the Ssl1 variants were solved, which show that none of the amino acid side chains coordinate to the Cu. Instead, a water molecule is found in the axial coordination site, which support the spectroscopic data. Our findings highlight the importance of combining structural and spectroscopic methods to investigate the effect of amino acid exchange on multicopper oxidases.


  • Organizational Affiliation

    Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf, 40225, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper oxidaseA [auth AAA],
B [auth BBB],
C [auth CCC]
325Streptomyces sviceus ATCC 29083Mutation(s): 1 
Gene Names: SSEG_02446
UniProt
Find proteins for B5HSR1 (Streptomyces sviceus (strain ATCC 29083 / DSM 924 / JCM 4929 / NBRC 13980 / NCIMB 11184 / NRRL 5439 / UC 5370))
Explore B5HSR1 
Go to UniProtKB:  B5HSR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5HSR1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GLU-HIS-SERD [auth FFF]3Streptomyces sviceusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth AAA],
I [auth AAA],
P [auth CCC]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU
Query on CU

Download Ideal Coordinates CCD File 
E [auth AAA]
F [auth AAA]
G [auth AAA]
J [auth BBB]
K [auth BBB]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.4α = 90
b = 104.24β = 90
c = 162.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-12-04
    Changes: Database references, Structure summary