6RWF

The dissociation mechanism of processive cellulases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The dissociation mechanism of processive cellulases.

Vermaas, J.V.Kont, R.Beckham, G.T.Crowley, M.F.Gudmundsson, M.Sandgren, M.Stahlberg, J.Valjamae, P.Knott, B.C.

(2019) Proc.Natl.Acad.Sci.USA 116: 23061-23067

  • DOI: 10.1073/pnas.1913398116

  • PubMed Abstract: 
  • Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many su ...

    Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many sugar molecules in a processive manner without dissociating from the substrate. Within the complete processive cycle of CBHs, dissociation from the cellulose substrate is rate limiting, but the molecular mechanism of this step is unknown. Here, we present a direct comparison of potential molecular mechanisms for dissociation via Hamiltonian replica exchange molecular dynamics of the model fungal CBH, Trichoderma reesei Cel7A. Computational rate estimates indicate that stepwise cellulose dethreading from the binding tunnel is 4 orders of magnitude faster than a clamshell mechanism, in which the substrate-enclosing loops open and release the substrate without reversing. We also present the crystal structure of a disulfide variant that covalently links substrate-enclosing loops on either side of the substrate-binding tunnel, which constitutes a CBH that can only dissociate via stepwise dethreading. Biochemical measurements indicate that this variant has a dissociation rate constant essentially equivalent to the wild type, implying that dethreading is likely the predominant mechanism for dissociation.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia 51010.,Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-75651 Uppsala, Sweden.,Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401.,Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401; brandon.knott@nrel.gov.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucanase
A
432Hypocrea jecorina (strain QM6a)Mutation(s): 2 
Gene Names: cel7a
EC: 3.2.1.-
Find proteins for G0RVK1 (Hypocrea jecorina (strain QM6a))
Go to UniProtKB:  G0RVK1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.363α = 90.00
b = 51.632β = 96.31
c = 65.590γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United StatesDE-AC36-08GO28308

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Type: Data collection, Database references
  • Version 1.2: 2019-11-20
    Type: Database references