1KYA | pdb_00001kya

ACTIVE LACCASE FROM TRAMETES VERSICOLOR COMPLEXED WITH 2,5-XYLIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.276 (Depositor) 
  • R-Value Work: 
    0.253 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1KYA

This is version 1.5 of the entry. See complete history

Literature

Crystal structure of a four-copper laccase complexed with an arylamine: insights into substrate recognition and correlation with kinetics.

Bertrand, T.Jolivalt, C.Briozzo, P.Caminade, E.Joly, N.Madzak, C.Mougin, C.

(2002) Biochemistry 41: 7325-7333

  • DOI: https://doi.org/10.1021/bi0201318
  • Primary Citation Related Structures: 
    1KYA

  • PubMed Abstract: 

    Laccases are multicopper oxidases that catalyze the oxidation of a wide range of phenols or arylamines, and their use in industrial oxidative processes is increasing. We purified from the white rot fungus Trametes versicolor a laccase that exists as five different isozymes, depending on glycosylation. The 2.4 A resolution structure of the most abundant isozyme of the glycosylated enzyme was solved. The four copper atoms are present, and it is the first crystal structure of a laccase in its active form. The crystallized enzyme binds 2,5-xylidine, which was used as a laccase inducer in the fungus culture. This arylamine is a very weak reducing substrate of the enzyme. The cavity enclosing 2,5-xylidine is rather wide, allowing the accommodation of substrates of various sizes. Several amino acid residues make hydrophobic interactions with the aromatic ring of the ligand. In addition, two charged or polar residues interact with its amino group. The first one is an histidine that also coordinates the copper that functions as the primary electron acceptor. The second is an aspartate conserved among fungal laccases. The purified enzyme can oxidize various hydroxylated compounds of the phenylurea family of herbicides that we synthesized. These phenolic substrates have better affinities at pH 5 than at pH 3, which could be related to the 2,5-xylidine binding by the aspartate. This is the first high-resolution structure of a multicopper oxidase complexed to a reducing substrate. It provides a model for engineering laccases that are either more efficient or with a wider substrate specificity.


  • Organizational Affiliation
    • Laboratoire d'Enzymologie et Biochimie Structurales, UPR 9063 du CNRS, 91198 Gif-sur-Yvette Cedex, France.

Macromolecule Content 

  • Total Structure Weight: 221.72 kDa 
  • Atom Count: 16,286 
  • Modeled Residue Count: 1,996 
  • Deposited Residue Count: 1,996 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LACCASE
A, B, C, D
499Trametes versicolorMutation(s): 0 
EC: 1.10.3.2
UniProt
Find proteins for Q96UT7 (Trametes versicolor)
Explore Q96UT7 
Go to UniProtKB:  Q96UT7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96UT7
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
S [auth B],
T [auth B],
U [auth B],
UA [auth D],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
XYD

Query on XYD



Download:Ideal Coordinates CCD File
HA [auth B],
HB [auth D],
R [auth A],
TA [auth C]
2,5-DIMETHYLANILINE
C8 H11 N
VOWZNBNDMFLQGM-UHFFFAOYSA-N
PYE

Query on PYE



Download:Ideal Coordinates CCD File
DA [auth B]
EA [auth B]
EB [auth D]
FA [auth B]
FB [auth D]
DA [auth B],
EA [auth B],
EB [auth D],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
P [auth A],
Q [auth A]
TETRAHYDROPYRAN
C5 H10 O
DHXVGJBLRPWPCS-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth D]
BA [auth B]
BB [auth D]
CA [auth B]
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CA [auth B],
CB [auth D],
DB [auth D],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
Z [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.276 (Depositor) 
  • R-Value Work:  0.253 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.72α = 90
b = 110.52β = 103.436
c = 123.201γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2024-10-30
    Changes: Structure summary