5NQ9 | pdb_00005nq9

Crystal structure of laccases from Pycnoporus sanguineus, izoform II, monoclinic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 
    0.246 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Structural studies of two thermostable laccases from the white-rot fungus Pycnoporus sanguineus.

Orlikowska, M.de J Rostro-Alanis, M.Bujacz, A.Hernandez-Luna, C.Rubio, R.Parra, R.Bujacz, G.

(2018) Int J Biol Macromol 107: 1629-1640

  • DOI: https://doi.org/10.1016/j.ijbiomac.2017.10.024
  • Primary Citation Related Structures: 
    5NQ7, 5NQ8, 5NQ9

  • PubMed Abstract: 

    Laccases are enzymes that have the ability to catalyze the oxidation of a wide spectrum of phenolic compounds with the four-electron reduction of molecular oxygen to water. The active site of those proteins contains four copper ions, classified into three types. Laccases are interesting enzymes for study from the point of view of their structure, function and application because of their role in lignin degradation. Structural studies of two thermostable laccases produced by the strain Pycnoporus sanguineus CS43 (PsLacI and PsLacII) were performed. Both isoforms of PsLac show high thermal stability, at 60°C and 50°C, respectively, and they remained active at a high concentration of organic solvents. However, PsLacI has a higher thermal and pH stability and tolerance against inhibitors, and is a more efficient catalyst for ABTS and DMP (laccases substrate) than PsLacII. Based on the determined crystal structures we achieved insights into the structural factors relevant for the enzymatic properties of PsLacI and PsLacII. N-glycosylation site Asn354, which is very often present in structures of fungal laccases from other species, was not present in PsLac. This observation may be of particular significance due to the close distance between Asn354 and the substrate-binding pocket. This results in better access to the hydrophobic cavity for a particular substrate. Furthermore, we identified significant differences in the region of substrate-binding pocket, which confer PsLacI a markedly better performance than PsLacII.


  • Organizational Affiliation
    • Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-924 Lodz, Stefanowskiego 4/10, Poland.

Macromolecule Content 

  • Total Structure Weight: 117.23 kDa 
  • Atom Count: 7,992 
  • Modeled Residue Count: 994 
  • Deposited Residue Count: 1,036 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Laccase, izoform IIA,
B [auth C]
518Trametes sanguineaMutation(s): 0 
EC: 1.10.3.2
UniProt
Find proteins for A0A2H4A2Q2 (Trametes sanguinea)
Explore A0A2H4A2Q2 
Go to UniProtKB:  A0A2H4A2Q2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2H4A2Q2
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]5N-Glycosylation
Glycosylation Resources
GlyTouCan: G27747YT
GlyCosmos: G27747YT
GlyGen: G27747YT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
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
E, G
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
EA [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
FA [auth C]
GA [auth C]
HA [auth C]
M [auth A]
N [auth A]
FA [auth C],
GA [auth C],
HA [auth C],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
H [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
MA [auth C],
NA [auth C],
X [auth A],
Y [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
IA [auth C]
JA [auth C]
KA [auth C]
LA [auth C]
Q [auth A]
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
PER

Query on PER



Download:Ideal Coordinates CCD File
L [auth A],
Z [auth C]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free:  0.246 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.459α = 90
b = 61.962β = 109.82
c = 103.307γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata 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: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary