5Z1X

Crystal Structure of Laccase from Cerrena sp. RSD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Kinetic analysis and structural studies of a high-efficiency laccase fromCerrenasp. RSD1.

Wu, M.H.Lee, C.C.Hsiao, A.S.Yu, S.M.Wang, A.H.J.Ho, T.D.

(2018) FEBS Open Bio 8: 1230-1246

  • DOI: https://doi.org/10.1002/2211-5463.12459
  • Primary Citation of Related Structures:  
    5Z1X

  • PubMed Abstract: 

    A high-efficiency laccase, DLac, was isolated from Cerrena sp. RSD1. The kinetic studies indicate that DLac is a diffusion-limited enzyme. The crystal structure of DLac was determined to atomic resolution, and its overall structure shares high homology to monomeric laccases, but displays unique substrate-binding loops from those in other laccases. The substrate-binding residues with small side chain and the short substrate-binding loop IV broaden the substrate-binding cavity and may facilitate large substrate diffusion. Unlike highly glycosylated fungal laccases, the less-glycosylated DLac contains one highly conserved glycosylation site at N432 and an unique glycosylation site at N468. The N -glycans stabilize the substrate-binding loops and the protein structure, and the first N -acetylglucosamine is crucial for the catalytic efficiency. Additionally, a fivefold increase in protein yield is achieved via the submerged culture method for industrial applications. The atomic coordinates of the structure of DLac from Cerrena sp. RSD1 and structural factors have been deposited in the RCSB Protein Data Bank (PDB ID: 5Z1X).


  • Organizational Affiliation

    Institute of Plant and Microbial Biology Academia Sinica Taipei Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Laccase
A, B
495CerrenaMutation(s): 0 
EC: 1.10.3.2
UniProt
Find proteins for A0A3F2YLU5 (Cerrena)
Explore A0A3F2YLU5 
Go to UniProtKB:  A0A3F2YLU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3F2YLU5
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
P [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
Q [auth B]
R [auth B]
F [auth A],
G [auth A],
H [auth A],
Q [auth B],
R [auth B],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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I [auth A],
J [auth A],
T [auth B],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU

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K [auth A]
L [auth A]
M [auth A]
N [auth A]
V [auth B]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
OXY
Query on OXY

Download Ideal Coordinates CCD File 
O [auth A],
Z [auth B]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.626α = 90
b = 88.795β = 90
c = 147.815γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary