5AA7

Structural and functional characterization of a chitin-active 15.5 kDa lytic polysaccharide monooxygenase domain from a modular chitinase from Jonesia denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and Functional Characterization of a Small Chitin-Active Lytic Polysaccharide Monooxygenase Domain of a Multi-Modular Chitinase from Jonesia Denitrificans.

Mekasha, S.Forsberg, Z.Dalhus, B.Bacik, J.Choudhary, S.Schmidt-Dannert, C.Vaaje-Kolstad, G.Eijsink, V.G.H.

(2016) FEBS Lett. 590: 34

  • DOI: 10.1002/1873-3468.12025

  • PubMed Abstract: 
  • Lytic polysaccharide monooxygenases (LPMOs) boost enzymatic depolymerization of recalcitrant polysaccharides, such as chitin and cellulose. We have studied a chitin-active LPMO domain (JdLPMO10A) that is considerably smaller (15.5 kDa) than all struc ...

    Lytic polysaccharide monooxygenases (LPMOs) boost enzymatic depolymerization of recalcitrant polysaccharides, such as chitin and cellulose. We have studied a chitin-active LPMO domain (JdLPMO10A) that is considerably smaller (15.5 kDa) than all structurally characterized LPMOs so far and that is part of a modular protein containing a GH18 chitinase. The 1.55 Å resolution structure revealed deletions of interacting loops that protrude from the core β-sandwich scaffold in larger LPMO10s. Despite these deletions, the enzyme is active on alpha- and beta-chitin, and the chitin-binding surface previously described for larger LPMOs is fully conserved. JdLPMO10A may represent a minimal scaffold needed to catalyse the powerful LPMO reaction.


    Organizational Affiliation

    Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, NM, USA.,Department of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, Rikshospitalet, Norway.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, USA.,Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHITINASE
A, B
142Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134)Mutation(s): 0 
EC: 3.2.1.14
Find proteins for C7R4I0 (Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134))
Go to UniProtKB:  C7R4I0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU1
Query on CU1

Download SDF File 
Download CCD File 
A, B
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.760α = 90.00
b = 74.330β = 90.00
c = 119.230γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
SHELXEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2016-04-06
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Data collection