4YZP

Crystal structure of a tri-modular GH5 (subfamily 4) endo-beta-1, 4-glucanase from Bacillus licheniformis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism.

Liberato, M.V.Silveira, R.L.Prates, E.T.de Araujo, E.A.Pellegrini, V.O.Camilo, C.M.Kadowaki, M.A.de O.Neto, M.Popov, A.Skaf, M.S.Polikarpov, I.

(2016) Sci Rep 6: 23473-23473

  • DOI: https://doi.org/10.1038/srep23473
  • Primary Citation of Related Structures:  
    4YZP, 4YZT

  • PubMed Abstract: 

    Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.


  • Organizational Affiliation

    São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590 São Paulo, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellulose hydrolase536Bacillus licheniformisMutation(s): 0 
Gene Names: cel5C
EC: 3.2.1.4
UniProt
Find proteins for Q65JI7 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46))
Explore Q65JI7 
Go to UniProtKB:  Q65JI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65JI7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.7α = 90
b = 90.7β = 90
c = 120.63γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2008/56255-9
Sao Paulo Research Foundation (FAPESP)Brazil2009/52840-7
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil490022/2009-0
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil301981/2011-6

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description