5Z3K

Crystal structure of glucosidase from Croceicoccus marinus at 1.8 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Insights Into CmGH1, a Novel GH39 Family beta-Glucosidase From Deep-Sea Bacterium.

Shen, Y.Li, Z.Huo, Y.Y.Bao, L.Gao, B.Xiao, P.Hu, X.Xu, X.W.Li, J.

(2019) Front Microbiol 10: 2922-2922

  • DOI: https://doi.org/10.3389/fmicb.2019.02922
  • Primary Citation of Related Structures:  
    5Z3K

  • PubMed Abstract: 

    Glucosidases play key roles in many diseases and are limiting enzymes during cellulose degradation, which is an important part of global carbon cycle. Here, we identified a novel β-glucosidase, CmGH1, isolated from marine bacterium Croceicoccus marinus E4A9 T . In spite of its high sequence and structural similarity with β-xylosidase family members, CmGH1 had enzymatic activity toward p -nitrophenyl-β-D-glucopyranoside ( p- NPG) and cellobiose. The K m and K cat values of CmGH1 toward p- NPG were 0.332 ± 0.038 mM and 2.15 ± 0.081 min -1 , respectively. CmGH1 was tolerant to high concentration salts, detergents, as well as many kinds of organic solvents. The crystal structure of CmGH1 was resolved with a 1.8 Å resolution, which showed that CmGH1 was composed of a canonical (α/β) 8 -barrel catalytic domain and an auxiliary β-sandwich domain. Although no canonical catalytic triad residues were found in CmGH1, structural comparison and mutagenesis analysis suggested that residues Gln157 and Tyr264 of CmGH1 were the active sites. Mutant Q157E significantly increased its hydrolase activity up to 15-fold, whereas Y264E totally abolished its enzymatic activity. These results might provide new insights into understanding the different catalytic mechanism during evolution for β-glucosidases and β-xylosidases.


  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
glucosidase
A, B
485Croceicoccus marinusMutation(s): 0 
Gene Names: A9D14_15590
UniProt
Find proteins for A0A1Z1FG87 (Croceicoccus marinus)
Explore A0A1Z1FG87 
Go to UniProtKB:  A0A1Z1FG87
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z1FG87
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.911α = 90
b = 95.911β = 98.71
c = 100.908γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data collection
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary