8GF3 | pdb_00008gf3

Crystallographic structure from BlMan5_7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.150 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.128 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.129 (Depositor) 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Unravelling biochemical and structural features of Bacillus licheniformis GH5 mannanase using site-directed mutagenesis and high-resolution protein crystallography studies.

Briganti, L.Manzine, L.R.de Mello Capetti, C.C.de Araujo, E.A.de Oliveira Arnoldi Pellegrini, V.Guimaraes, F.E.G.de Oliveira Neto, M.Polikarpov, I.

(2024) Int J Biol Macromol 274: 133182-133182

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.133182
  • Primary Citation of Related Structures:  
    8GF3

  • PubMed Abstract: 

    Glycoside hydrolase family 5 (GH5) encompasses enzymes with several different activities, including endo-1,4-β-mannosidases. These enzymes are involved in mannan degradation, and have a number of biotechnological applications, such as mannooligosaccharide prebiotics production, stain removal and dyes decolorization, to name a few. Despite the importance of GH5 enzymes, only a few members of subfamily 7 were structurally characterized. In the present work, biochemical and structural characterization of Bacillus licheniformis GH5 mannanase, BlMan5_7 were performed and the enzyme cleavage pattern was analyzed, showing that BlMan5_7 requires at least 5 occupied subsites to perform efficient hydrolysis. Additionally, crystallographic structure at 1.3 Å resolution was determined and mannoheptaose (M7) was docked into the active site to investigate the interactions between substrate and enzyme through molecular dynamic (MD) simulations, revealing the existence of a - 4 subsite, which might explain the generation of mannotetraose (M4) as an enzyme product. Biotechnological application of the enzyme in stain removal was investigated, demonstrating that BlMan5_7 addition to washing solution greatly improves mannan-based stain elimination.


  • Organizational Affiliation
    • Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GH5 Mannanase365Bacillus licheniformisMutation(s): 1 
Gene Names: celDBL01229
UniProt
Find proteins for Q65JI6 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46))
Explore Q65JI6 
Go to UniProtKB:  Q65JI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65JI6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.150 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.128 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.129 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.722α = 90
b = 164.744β = 90
c = 84.711γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil306852/2021-7
Sao Paulo Research Foundation (FAPESP)Brazil2021/08780-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 2.0: 2024-07-31
    Changes: Advisory, Atomic model, Data collection, Database references, Polymer sequence, Source and taxonomy, Structure summary