5W11

Biochemical and structural insights into the catalytic mechanism of thermostable cellobiohydrolase Cel7A from industrially relevant fungus Myceliophthora thermophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.311 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Biochemical and structural insights into a thermostable cellobiohydrolase from Myceliophthora thermophila.

Kadowaki, M.A.S.Higasi, P.de Godoy, M.O.Prade, R.A.Polikarpov, I.

(2018) FEBS J. 285: 559-579

  • DOI: 10.1111/febs.14356

  • PubMed Abstract: 
  • Cellobiohydrolases hydrolyze cellulose, a linear polymer with glucose monomers linked exclusively by β-1,4 glycosidic linkages. The widespread hydrogen bonding network tethers individual cellulose polymers forming crystalline cellulose, which prevent ...

    Cellobiohydrolases hydrolyze cellulose, a linear polymer with glucose monomers linked exclusively by β-1,4 glycosidic linkages. The widespread hydrogen bonding network tethers individual cellulose polymers forming crystalline cellulose, which prevent the access of hydrolytic enzymes and water molecules. The most abundant enzyme secreted by Myceliophthora thermophila M77 in response to the presence of biomass is the cellobiohydrolase MtCel7A, which is composed by a GH7-catalytic domain (CD), a linker, and a CBM1-type carbohydrate-binding module. GH7 cellobiohydrolases have been studied before, and structural models have been proposed. However, currently available GH7 crystal structures only define separate catalytic domains and/or cellulose-binding modules and do not include the full-length structures that are involved in shaping the catalytic mode of operation. In this study, we determined the 3D structure of catalytic domain using X-ray crystallography and retrieved the full-length enzyme envelope via small-angle X-ray scattering (SAXS) technique. The SAXS data reveal a tadpole-like molecular shape with a rigid linker connecting the CD and CBM. Our biochemical studies show that MtCel7A has higher catalytic efficiency and thermostability as well as lower processivity when compared to the well-studied TrCel7A from Trichoderma reesei. Based on a comparison of the crystallographic structures of CDs and their molecular dynamic simulations, we demonstrate that MtCel7A has considerably higher flexibility than TrCel7A. In particular, loops that cover the active site are more flexible and undergo higher conformational fluctuations, which might account for decreased processivity and enhanced enzymatic efficiency. Our statistical coupling analysis suggests co-evolution of amino acid clusters comprising the catalytic site of MtCel7A, which correlate with the steps in the catalytic cycle of the enzyme.


    Organizational Affiliation

    São Carlos Institute of Physics, University of São Paulo, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucanase
A, B
440Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799)Mutation(s): 0 
EC: 3.2.1.-
Find proteins for G2Q665 (Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Go to UniProtKB:  G2Q665
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
144
Query on 144

Download SDF File 
Download CCD File 
B
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
C4 H12 N O3
DRDCQJADRSJFFD-UHFFFAOYSA-N
 Ligand Interaction
CTR
Query on CTR

Download SDF File 
Download CCD File 
A, B
CELLOTRIOSE
Dextrin
C18 H32 O16
FYGDTMLNYKFZSV-RZDZXANRSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.311 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.619α = 90.00
b = 93.261β = 100.46
c = 69.679γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FAPESPBrazil2011/20505-4

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-20
    Type: Database references
  • Version 1.2: 2018-02-14
    Type: Database references