6IBJ

Copper binding protein from Laetisaria arvalis (LaX325)

• PDB DOI:  https://doi.org/10.2210/pdb6IBJ/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Laetisaria arvalis
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2018-11-30 Released: 2019-11-13 
• Deposition Author(s): Frandsen, K.E.H., Tandrup, T., Labourel, A., Haon, M., Berrin, J.-G., Lo Leggio, L.
• Funding Organization(s): Novo Nordisk Foundation, The Carlsberg Foundation, European Communitys Seventh Framework Programme

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

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

• PubMed: 31932718 
• 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.

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Organizational Affiliation: 

INRA, Biodiversité et Biotechnologie Fongiques (BBF), UMR1163, Aix Marseille Université, Marseille, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.61 kDa 
• Atom Count: 1,237 
• Modelled Residue Count: 150 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Auxiliary activity CAZyme	A	155	Laetisaria arvalis	Mutation(s): 0
UniProt
Find proteins for A0A4P9I8G4 (Laetisaria arvalis) Explore A0A4P9I8G4  Go to UniProtKB:  A0A4P9I8G4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.92	α = 90
b = 74.92	β = 90
c = 64.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Frandsen, K.E.H., Tandrup, T., Labourel, A., Haon, M., Berrin, J.-G., Lo Leggio, L.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NF17SA0027704
The Carlsberg Foundation	Denmark	CF16-0673 & CF17-0533
European Communitys Seventh Framework Programme	France	grant agreement 609398

Revision History  

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