4M1R | pdb_00004m1r

Structure of a novel cellulase 5 from a sugarcane soil metagenomic library


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.173 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.131 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 
    0.133 (Depositor) 

wwPDB Validation 3D Report Full Report

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Literature

Structure and function of a novel cellulase 5 from sugarcane soil metagenome.

Alvarez, T.M.Paiva, J.H.Ruiz, D.M.Cairo, J.P.Pereira, I.O.Paixao, D.A.de Almeida, R.F.Tonoli, C.C.Ruller, R.Santos, C.R.Squina, F.M.Murakami, M.T.

(2013) PLoS One 8: e83635-e83635

  • DOI: https://doi.org/10.1371/journal.pone.0083635
  • Primary Citation Related Structures: 
    4M1R

  • PubMed Abstract: 

    Cellulases play a key role in enzymatic routes for degradation of plant cell-wall polysaccharides into simple and economically-relevant sugars. However, their low performance on complex substrates and reduced stability under industrial conditions remain the main obstacle for the large-scale production of cellulose-derived products and biofuels. Thus, in this study a novel cellulase with unusual catalytic properties from sugarcane soil metagenome (CelE1) was isolated and characterized. The polypeptide deduced from the celE1 gene encodes a unique glycoside hydrolase domain belonging to GH5 family. The recombinant enzyme was active on both carboxymethyl cellulose and β-glucan with an endo-acting mode according to capillary electrophoretic analysis of cleavage products. CelE1 showed optimum hydrolytic activity at pH 7.0 and 50 °C with remarkable activity at alkaline conditions that is attractive for industrial applications in which conventional acidic cellulases are not suitable. Moreover, its three-dimensional structure was determined at 1.8 Å resolution that allowed the identification of an insertion of eight residues in the β8-α8 loop of the catalytic domain of CelE1, which is not conserved in its psychrophilic orthologs. This 8-residue-long segment is a prominent and distinguishing feature of thermotolerant cellulases 5 suggesting that it might be involved with thermal stability. Based on its unconventional characteristics, CelE1 could be potentially employed in biotechnological processes that require thermotolerant and alkaline cellulases.


  • Organizational Affiliation
    • Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil.

Macromolecule Content 

  • Total Structure Weight: 63.79 kDa 
  • Atom Count: 4,924 
  • Modeled Residue Count: 592 
  • Deposited Residue Count: 592 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cellulase 5
A, B
296soil metagenomeMutation(s): 0 
EC: 3.2.1.4

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.173 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.131 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 0.133 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.888α = 90
b = 87.512β = 98.55
c = 66.63γ = 90
Software Package:
Software NamePurpose
NatXraydata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations