8S3L | pdb_00008s3l

X-ray crystal structure of LsAA9A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.262 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Literature

Anions and citrate inhibit LsAA9A, a lytic polysaccharide monooxygenase (LPMO).

Di Domenico, V.Theibich, Y.Brander, S.Berrin, J.G.Johansen, K.S.Frandsen, K.E.H.Lo Leggio, L.

(2025) FEBS J 292: 4375-4389

  • DOI: https://doi.org/10.1111/febs.70138
  • Primary Citation of Related Structures:  
    8S3F, 8S3L, 9EQE

  • PubMed Abstract: 

    Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes that break the glycosidic linkage in recalcitrant polysaccharides such as cellulose and chitin. The LPMO LsAA9A (AA9 family lytic polysaccharide monooxygenase A) from the basidiomycete fungus Lentinus similis is biochemically and structurally well characterized, with crystallographic complexes with oligosaccharides having been obtained. Chloride ions from the crystallization solution are known to bind to the LsAA9A-substrate complex in crystals at the copper equatorial coordinating position, where activation of the co-substrate oxygen species is expected. An investigation of the effect of high concentration salts on LsAA9A activity showed that salts containing chloride and other halide anions, except for fluoride, had a clear inhibitory effect on the activity at concentrations > 100 mm, although chloride ions are known to increase the LPMO affinity for oligosaccharide binding. Surprisingly, LsAA9A crystals can be transferred for short times to considerably different chemical environments, allowing crystallographic analysis at reduced chloride concentrations. Unfortunately, these washing steps do not eliminate the chloride binding at the copper equatorial coordinating position. Furthermore, we observed that citrate buffer, also present, bound under these changed chemical conditions at the copper active site. This interaction completely blocks access to the oligosaccharide substrate and is additionally supported here by citrate inhibition of LsAA9A activities against azurine cross-linked hydroxyethylcellulose (AZCL-HEC), tamarind xyloglucan, and cellopentaose. The conclusions from our study indicate that citrate should be absolutely avoided in LPMO research, not only because of possible abstraction of copper ions from the LPMO active site but also because it might directly compete with binding of LPMOs to their target substrates.


  • Organizational Affiliation
    • Department of Chemistry, University of Copenhagen, Denmark.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-beta-1,4-glucanase D235Panus similisMutation(s): 0 
EC: 3.2.1.4 (PDB Primary Data), 1.14.99.56 (UniProt)
UniProt
Find proteins for A0A0S2GKZ1 (Panus similis)
Explore A0A0S2GKZ1 
Go to UniProtKB:  A0A0S2GKZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S2GKZ1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
B
4N/A
Glycosylation Resources
GlyTouCan:  G00025MO
GlyCosmos:  G00025MO
GlyGen:  G00025MO
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.262 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.72α = 90
b = 126.72β = 90
c = 126.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF17SA0027704
Novo Nordisk FoundationDenmarkNNF21OC0071799
Danish Council for Independent ResearchDenmark8021-00273B
The Carlsberg FoundationDenmarkCF16-0673
The Carlsberg FoundationDenmarkCF17-0533

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references