6IBI | pdb_00006ibi

Copper binding protein from Laetisaria arvalis (LaX325)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.271 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6IBI

Ligand Structure Quality Assessment 


This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 73.48 kDa 
  • Atom Count: 5,546 
  • Modeled Residue Count: 607 
  • Deposited Residue Count: 620 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Auxiliary activity CAZyme
A, B, C, D
155Laetisaria arvalisMutation(s): 0 
UniProt
Find proteins for A0A4P9I8G4 (Waitea arvalis)
Explore A0A4P9I8G4 
Go to UniProtKB:  A0A4P9I8G4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4P9I8G4
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
FA [auth C],
L [auth A],
MA [auth D],
N [auth A],
W [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
F [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
F [auth A],
G [auth A],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
LA [auth D],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
M [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
EA [auth C],
V [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CU

Query on CU



Download:Ideal Coordinates CCD File
E [auth A],
GA [auth D],
O [auth B],
X [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.271 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.599α = 90
b = 84.635β = 90
c = 127.319γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
AutoSolphasing
PHASERphasing
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 Carslberg 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
  • Version 1.5: 2024-10-23
    Changes: Data collection, Database references, Refinement description, Structure summary