3V9E | pdb_00003v9e

Structure of the L499M mutant of the laccase from B.aclada


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.200 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3V9E

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Effect of the L499M mutation of the ascomycetous Botrytis aclada laccase on redox potential and catalytic properties.

Osipov, E.Polyakov, K.Kittl, R.Shleev, S.Dorovatovsky, P.Tikhonova, T.Hann, S.Ludwig, R.Popov, V.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2913-2923

  • DOI: https://doi.org/10.1107/S1399004714020380
  • Primary Citation Related Structures: 
    3SQR, 3V9E

  • PubMed Abstract: 

    Laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. These enzymes contain four Cu atoms per molecule organized into three sites: T1, T2 and T3. In all laccases, the T1 copper ion is coordinated by two histidines and one cysteine in the equatorial plane and is covered by the side chains of hydrophobic residues in the axial positions. The redox potential of the T1 copper ion influences the enzymatic reaction and is determined by the nature of the axial ligands and the structure of the second coordination sphere. In this work, the laccase from the ascomycete Botrytis aclada was studied, which contains conserved Ile491 and nonconserved Leu499 residues in the axial positions. The three-dimensional structures of the wild-type enzyme and the L499M mutant were determined by X-ray crystallography at 1.7 Å resolution. Crystals suitable for X-ray analysis could only be grown after deglycosylation. Both structures did not contain the T2 copper ion. The catalytic properties of the enzyme were characterized and the redox potentials of both enzyme forms were determined: E0 = 720 and 580 mV for the wild-type enzyme and the mutant, respectively. Since the structures of the wild-type and mutant forms are very similar, the change in the redox potential can be related to the L499M mutation in the T1 site of the enzyme.


  • Organizational Affiliation
    • A. N. Bach Institute of Biochemistry, Leninsky Prospect 33/2, Moscow 119071, Russian Federation.

Macromolecule Content 

  • Total Structure Weight: 66.43 kDa 
  • Atom Count: 4,780 
  • Modeled Residue Count: 539 
  • Deposited Residue Count: 580 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Laccase580Botrytis acladaMutation(s): 0 
EC: 1.10.3.2

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
K [auth A],
L [auth A],
M [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN

Query on MAN



Download:Ideal Coordinates CCD File
J [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.200 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.71α = 90
b = 113.56β = 108.74
c = 79.98γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 1.2: 2014-12-03
    Changes: Structure summary
  • Version 1.3: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary