6YDF

X-ray structure of LPMO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Oligosaccharide Binding and Thermostability of Two Related AA9 Lytic Polysaccharide Monooxygenases.

Tandrup, T.Tryfona, T.Frandsen, K.E.H.Johansen, K.S.Dupree, P.Lo Leggio, L.

(2020) Biochemistry 59: 3347-3358

  • DOI: 10.1021/acs.biochem.0c00312
  • Primary Citation of Related Structures:  
    6YDD, 6YDC, 6YDF, 6YDE, 6YDG

  • PubMed Abstract: 
  • Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that cleave polysaccharide substrates oxidatively. First discovered because of their action on recalcitrant crystalline substrates (chitin and cellulose), a number of LPMOs are ...

    Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that cleave polysaccharide substrates oxidatively. First discovered because of their action on recalcitrant crystalline substrates (chitin and cellulose), a number of LPMOs are now reported to act on soluble substrates, including oligosaccharides. However, crystallographic complexes with oligosaccharides have been reported for only a single LPMO so far, an enzyme from the basidiomycete fungus Lentinus similis ( Ls AA9_A). Here we present a more detailed comparative study of Ls AA9_A and an LPMO from the ascomycete fungus Collariella virescens ( Cv AA9_A) with which it shares 41.5% sequence identity. Ls AA9_A is considerably more thermostable than Cv AA9_A, and the structural basis for the difference has been investigated. We have compared the patterns of oligosaccharide cleavage and the patterns of binding in several new crystal structures explaining the basis for the product preferences of the two enzymes. Obtaining structural information about complexes of LPMOs with carbohydrates has proven to be very difficult in general judging from the structures reported in the literature thus far, and this can be attributed only partly to the low affinity for small substrates. We have thus evaluated the use of differential scanning fluorimetry as a guide to obtaining complex structures. Furthermore, an analysis of crystal packing of LPMOs and glycoside hydrolases corroborates the hypothesis that active site occlusion is a very significant problem for LPMO-substrate interaction analysis by crystallography, due to their relatively flat and extended substrate binding sites.


    Organizational Affiliation

    Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK Copenhagen, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LPMO lytic polysaccharide monooxygenaseAB252Collariella virescensMutation(s): 0 
Gene Names: aa9
Find proteins for A0A223GEC9 (Collariella virescens)
Explore A0A223GEC9 
Go to UniProtKB:  A0A223GEC9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HIC
Query on HIC

Download CCD File 
A, B
4-METHYL-HISTIDINE
C7 H11 N3 O2
BRMWTNUJHUMWMS-LURJTMIESA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CU
Query on CU

Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
A,BL-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.12α = 90
b = 39.39β = 93.78
c = 119.93γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF17SA0027704

Revision History 

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references