5ACG | pdb_00005acg

X-ray Structure of LPMO

• PDB DOI: https://doi.org/10.2210/pdb5ACG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Panus similis
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2015-08-17 Released: 2016-03-02 
• Deposition Author(s): Frandsen, K.E.H., Poulsen, J.N., Tovborg, M., Johansen, K.S., Lo Leggio, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.208 (Depositor) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases.

Frandsen, K.E., Simmons, T.J., Dupree, P., Poulsen, J.C., Hemsworth, G.R., Ciano, L., Johnston, E.M., Tovborg, M., Johansen, K.S., von Freiesleben, P., Marmuse, L., Fort, S., Cottaz, S., Driguez, H., Henrissat, B., Lenfant, N., Tuna, F., Baldansuren, A., Davies, G.J., Lo Leggio, L., Walton, P.H.

(2016) Nat Chem Biol 12: 298-303

• PubMed: 26928935 
• DOI: https://doi.org/10.1038/nchembio.2029
• Primary Citation Related Structures: 
  5ACF, 5ACG, 5ACH, 5ACI, 5ACJ


• PubMed Abstract: 
  

  Lytic polysaccharide monooxygenases (LPMOs) are copper-containing enzymes that oxidatively break down recalcitrant polysaccharides such as cellulose and chitin. Since their discovery, LPMOs have become integral factors in the industrial utilization of biomass, especially in the sustainable generation of cellulosic bioethanol. We report here a structural determination of an LPMO-oligosaccharide complex, yielding detailed insights into the mechanism of action of these enzymes. Using a combination of structure and electron paramagnetic resonance spectroscopy, we reveal the means by which LPMOs interact with saccharide substrates. We further uncover electronic and structural features of the enzyme active site, showing how LPMOs orchestrate the reaction of oxygen with polysaccharide chains.

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Organizational Affiliation: 
• Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
Department of Biochemistry, University of Cambridge, Cambridge, UK.
Department of Chemistry, University of York, York, UK.
Novozymes A/S, Bagsvaerd, Denmark.
Centre de Recherches sur les Macromolecules Végétales (CERMAV), Université de Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Grenoble, France.
Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France.
Institut National de la Recherche Agronomique (INRA), AFMB, Marseille, France.
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
Engineering and Physical Sciences Research Council (EPSRC) National EPR Facility, School of Chemistry and Photon Science Institute, University of Manchester, Manchester, UK.

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: 25.81 kDa 
• Atom Count: 2,186 
• Modeled Residue Count: 235 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYTIC POLYSACCHARIDE MONOOXYGENASE	A	235	Panus similis	Mutation(s): 0  EC: 1.14.99.56
UniProt
Find proteins for A0A0S2GKZ1 (Panus similis) Explore A0A0S2GKZ1  Go to UniProtKB:  A0A0S2GKZ1
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.208 (Depositor) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.24	α = 90
b = 125.24	β = 90
c = 125.24	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Frandsen, K.E.H., Poulsen, J.N., Tovborg, M., Johansen, K.S., Lo Leggio, L.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2016-03-30
  Changes: Database references
• Version 1.3: 2018-01-17
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.5: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary