4ALR

X-Ray photoreduction of Polysaccharide monooxygenase CBM33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Electronic Snapshots During the Transition from a Cu(II) to Cu(I) Metal Center of a Lytic Polysaccharide Monooxygenase by X-Ray Photo-Reduction.

Gudmundsson, M.Kim, S.Wu, M.Ishida, T.Haddad Momeni, M.Vaaje-Kolstad, G.Lundberg, D.Royant, A.Stahlberg, J.Eijsink, V.G.Beckham, G.T.Sandgren, M.

(2014) J.Biol.Chem. 289: 18782

  • DOI: 10.1074/jbc.M114.563494
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of enzymes that employ a copper-mediated, oxidative mechanism to cleave glycosidic bonds. The LPMO catalytic mechanism likely requires that molecular oxygen first binds to Cu ...

    Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of enzymes that employ a copper-mediated, oxidative mechanism to cleave glycosidic bonds. The LPMO catalytic mechanism likely requires that molecular oxygen first binds to Cu(I), but the oxidation state in many reported LPMO structures is ambiguous, and the changes in the LPMO active site required to accommodate both oxidation states of copper have not been fully elucidated. Here, a diffraction data collection strategy minimizing the deposited x-ray dose was used to solve the crystal structure of a chitin-specific LPMO from Enterococcus faecalis (EfaCBM33A) in the Cu(II)-bound form. Subsequently, the crystalline protein was photoreduced in the x-ray beam, which revealed structural changes associated with the conversion from the initial Cu(II)-oxidized form with two coordinated water molecules, which adopts a trigonal bipyramidal geometry, to a reduced Cu(I) form in a T-shaped geometry with no coordinated water molecules. A comprehensive survey of Cu(II) and Cu(I) structures in the Cambridge Structural Database unambiguously shows that the geometries observed in the least and most reduced structures reflect binding of Cu(II) and Cu(I), respectively. Quantum mechanical calculations of the oxidized and reduced active sites reveal little change in the electronic structure of the active site measured by the active site partial charges. Together with a previous theoretical investigation of a fungal LPMO, this suggests significant functional plasticity in LPMO active sites. Overall, this study provides molecular snapshots along the reduction process to activate the LPMO catalytic machinery and provides a general method for solving LPMO structures in both copper oxidation states.


    Organizational Affiliation

    From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHITIN BINDING PROTEIN
A
166Enterococcus faecalis (strain ATCC 700802 / V583)
Find proteins for Q838S1 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q838S1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

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

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.420α = 90.00
b = 48.578β = 90.00
c = 68.455γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2014-05-28
    Type: Database references
  • Version 1.2: 2014-08-13
    Type: Database references