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 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

Validation slider image for 4M1R

This is version 1.2 of the entry. See complete history. 

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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

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

View Full Validation Report



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