8U7G | pdb_00008u7g

Crystal structure of CIB_13 beta-galactosidase from Cuniculiplasma divulgatum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Moderately thermostable GH1 beta-glucosidases from hyperacidophilic archaeon Cuniculiplasma divulgatum S5.

Khusnutdinova, A.N.Tran, H.Devlekar, S.Distaso, M.A.Kublanov, I.V.Skarina, T.Stogios, P.Savchenko, A.Ferrer, M.Golyshina, O.V.Yakunin, A.F.Golyshin, P.N.

(2024) FEMS Microbiol Ecol 100

  • DOI: https://doi.org/10.1093/femsec/fiae114
  • Primary Citation of Related Structures:  
    8U7F, 8U7G

  • PubMed Abstract: 

    Family GH1 glycosyl hydrolases are ubiquitous in prokaryotes and eukaryotes and are utilized in numerous industrial applications, including bioconversion of lignocelluloses. In this study, hyperacidophilic archaeon Cuniculiplasma divulgatum (S5T=JCM 30642T) was explored as a source of novel carbohydrate-active enzymes. The genome of C. divulgatum encodes three GH1 enzyme candidates, from which CIB12 and CIB13 were heterologously expressed and characterized. Phylogenetic analysis of CIB12 and CIB13 clustered them with β-glucosidases from genuinely thermophilic archaea including Thermoplasma acidophilum, Picrophilus torridus, Sulfolobus solfataricus, Pyrococcus furiosus, and Thermococcus kodakarensis. Purified enzymes showed maximal activities at pH 4.5-6.0 (CIB12) and 4.5-5.5 (CIB13) with optimal temperatures at 50°C, suggesting a high-temperature origin of Cuniculiplasma spp. ancestors. Crystal structures of both enzymes revealed a classical (α/β)8 TIM-barrel fold with the active site located inside the barrel close to the C-termini of β-strands including the catalytic residues Glu204 and Glu388 (CIB12), and Glu204 and Glu385 (CIB13). Both enzymes preferred cellobiose over lactose as substrates and were classified as cellobiohydrolases. Cellobiose addition increased the biomass yield of Cuniculiplasma cultures growing on peptides by 50%, suggesting that the cellobiohydrolases expand the carbon substrate range and hence environmental fitness of Cuniculiplasma.


  • Organizational Affiliation
    • Centre for Environmental Biotechnology, School of Environmental and Natural Sciences, Bangor University, Bangor, LL57 2UW, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CIB_13 Beta-galactosidase
A, B
482Cuniculiplasma divulgatumMutation(s): 0 
Gene Names: CSP5_1651
UniProt
Find proteins for A0A1N5W3X4 (Cuniculiplasma divulgatum)
Explore A0A1N5W3X4 
Go to UniProtKB:  A0A1N5W3X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1N5W3X4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.8α = 90
b = 102.188β = 104.69
c = 97.542γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Database references, Structure summary