5N04

X-ray crystal structure of an LPMO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Unliganded and substrate bound structures of the cellooligosaccharide active lytic polysaccharide monooxygenase LsAA9A at low pH.

Frandsen, K.E.H.Poulsen, J.N.Tandrup, T.Lo Leggio, L.

(2017) Carbohydr Res 448: 187-190

  • DOI: 10.1016/j.carres.2017.03.010
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Lytic polysaccharide monooxygenases (LPMOs) have been found to be key components in microbial (bacterial and fungal) degradation of biomass. They are copper metalloenzymes that degrade polysaccharides oxidatively and act in synergy with glycoside hyd ...

    Lytic polysaccharide monooxygenases (LPMOs) have been found to be key components in microbial (bacterial and fungal) degradation of biomass. They are copper metalloenzymes that degrade polysaccharides oxidatively and act in synergy with glycoside hydrolases. Recently crystallographic studies carried out at pH 5.5 of the LPMO from Lentinus similis belonging to the fungal LPMO family AA9 have provided the first atomic resolution view of substrate-LPMO interactions. The LsAA9A structure presented here determined at pH 3.5 shows significant disorder of the active site in the absence of substrate ligand. Furthermore some differences are also observed in regards to substrate (cellohexaose) binding, although the major interaction with the N-terminal histidine remains unchanged.


    Organizational Affiliation

    Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark. Electronic address: leila@chem.ku.dk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Auxiliary activity 9A235Lentinus similisMutation(s): 0 
Find proteins for A0A0S2GKZ1 (Lentinus similis)
Explore A0A0S2GKZ1 
Go to UniProtKB:  A0A0S2GKZ1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CU
Query on CU

Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
AL-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.33α = 90
b = 125.33β = 90
c = 125.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Strategic ResearchDenmark12-134922
Danish Council for Strategic ResearchDenmark12-134923

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Database references
  • Version 1.3: 2019-08-14
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary