5ACH

X-ray Structure of LPMO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 

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This is version 1.4 of the entry. See complete history


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

  • DOI: 10.1038/nchembio.2029
  • Primary Citation of Related Structures:  
    5ACH, 5ACG, 5ACJ, 5ACI, 5ACF

  • 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, University of York, York, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYTIC POLYSACCHARIDE MONOOXYGENASEA235Panus similisMutation(s): 0 
UniProt
Find proteins for A0A0S2GKZ1 (Lentinus similis)
Explore A0A0S2GKZ1 
Go to UniProtKB:  A0A0S2GKZ1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
R [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
Q [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A] , C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , 
B [auth A],  C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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: 1.28 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.7α = 90
b = 124.7β = 90
c = 124.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Database references, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary