6IBH

Copper binding protein from Laetisaria arvalis (LaX325)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A fungal family of lytic polysaccharide monooxygenase-like copper proteins.

Labourel, A.Frandsen, K.E.H.Zhang, F.Brouilly, N.Grisel, S.Haon, M.Ciano, L.Ropartz, D.Fanuel, M.Martin, F.Navarro, D.Rosso, M.N.Tandrup, T.Bissaro, B.Johansen, K.S.Zerva, A.Walton, P.H.Henrissat, B.Leggio, L.L.Berrin, J.G.

(2020) Nat Chem Biol 16: 345-350

  • DOI: https://doi.org/10.1038/s41589-019-0438-8
  • Primary Citation of Related Structures:  
    6IBH, 6IBI, 6IBJ

  • PubMed Abstract: 

    Lytic polysaccharide monooxygenases (LPMOs) are copper-containing enzymes that play a key role in the oxidative degradation of various biopolymers such as cellulose and chitin. While hunting for new LPMOs, we identified a new family of proteins, defined here as X325, in various fungal lineages. The three-dimensional structure of X325 revealed an overall LPMO fold and a His brace with an additional Asp ligand to Cu(II). Although LPMO-type activity of X325 members was initially expected, we demonstrated that X325 members do not perform oxidative cleavage of polysaccharides, establishing that X325s are not LPMOs. Investigations of the biological role of X325 in the ectomycorrhizal fungus Laccaria bicolor revealed exposure of the X325 protein at the interface between fungal hyphae and tree rootlet cells. Our results provide insights into a family of copper-containing proteins, which is widespread in the fungal kingdom and is evolutionarily related to LPMOs, but has diverged to biological functions other than polysaccharide degradation.


  • Organizational Affiliation

    INRA, Biodiversité et Biotechnologie Fongiques (BBF), UMR1163, Aix Marseille Université, Marseille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Auxiliary activity CAZyme
A, B
155Laetisaria arvalisMutation(s): 0 
UniProt
Find proteins for A0A4P9I8G4 (Laetisaria arvalis)
Explore A0A4P9I8G4 
Go to UniProtKB:  A0A4P9I8G4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4P9I8G4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth A]
H [auth A]
C [auth A],
D [auth A],
E [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
O [auth B],
P [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
I [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CU
Query on CU

Download Ideal Coordinates CCD File 
F [auth A],
N [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.94α = 90
b = 67.59β = 97.94
c = 68.9γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNF17SA0027704
The Carlsberg FoundationDenmarkCF16-0673 & CF17-0533
European Communitys Seventh Framework ProgrammeFrancegrant agreement 609398

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Derived calculations
  • Version 1.2: 2020-01-22
    Changes: Database references
  • Version 1.3: 2020-03-04
    Changes: Data collection, Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary