3AYS

GH5 endoglucanase from a ruminal fungus in complex with cellotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Substrate binding of a GH5 endoglucanase from the ruminal fungus Piromyces rhizinflata.

Tseng, C.-W.Ko, T.-P.Guo, R.-T.Huang, J.-W.Wang, H.-C.Huang, C.-H.Cheng, Y.-S.Wang, A.H.-J.Liu, J.-R.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1189-1194

  • DOI: https://doi.org/10.1107/S1744309111032428
  • Primary Citation of Related Structures:  
    3AYR, 3AYS

  • PubMed Abstract: 

    The endoglucanase EglA from Piromyces rhizinflata found in cattle stomach belongs to the GH5 family of glycoside hydrolases. The crystal structure of the catalytic domain of EglA shows the (β/α)(8)-barrel fold typical of GH5 enzymes. Adjacent to the active site of EglA, a loop containing a disulfide bond not found in other similar structures may participate in substrate binding. Because the active site was blocked by the N-terminal His tag of a neighbouring protein molecule in the crystal, enzyme-substrate complexes could not be obtained by soaking but were prepared by cocrystallization. The E154A mutant structure with a cellotriose bound to the -3, -2 and -1 subsites shows an extensive hydrogen-bonding network between the enzyme and the substrate, along with a stacking interaction between Trp44 and the -3 sugar. A possible dimer was observed in the crystal structure, but retention of activity in the E242A mutant suggested that the enzyme probably does not function as a dimer in solution. On the other hand, the first 100 amino acids encoded by the original cDNA fragment are very similar to those in the last third of the (β/α)(8)-barrel fold, indicating that EglA comprises at least two catalytic domains acting in tandem.


  • Organizational Affiliation

    Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoglucanase376Piromyces rhizinflatusMutation(s): 1 
Gene Names: egla
EC: 3.2.1.4
UniProt
Find proteins for Q9URH5 (Piromyces rhizinflatus)
Explore Q9URH5 
Go to UniProtKB:  Q9URH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9URH5
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
B
3N/A
Glycosylation Resources
GlyTouCan:  G14338VK
GlyCosmos:  G14338VK
GlyGen:  G14338VK
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.204α = 90
b = 82.204β = 90
c = 221.856γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2012-04-11
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary