3ZZ1

Crystal structure of a glycoside hydrolase family 3 beta-glucosidase, Bgl1 from Hypocrea jecorina at 2.1A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Biochemical Characterization and Crystal Structures of a Fungal Family 3 Beta-Glucosidase, Cel3A from Hypocrea Jecorina.

Karkehabadi, S.Helmich, K.E.Kaper, T.Hansson, H.Mikkelsen, N.E.Gudmundsson, M.Piens, K.Fujdala, M.Banerjee, G.Scott-Craig, J.S.Walton, J.D.Phillips, G.N.J.Sandgren, M.

(2014) J Biol Chem 289: 31624

  • DOI: https://doi.org/10.1074/jbc.M114.587766
  • Primary Citation of Related Structures:  
    3ZYZ, 3ZZ1, 4I8D

  • PubMed Abstract: 

    Cellulase mixtures from Hypocrea jecorina are commonly used for the saccharification of cellulose in biotechnical applications. The most abundant β-glucosidase in the mesophilic fungus Hypocrea jecorina is HjCel3A, which hydrolyzes the β-linkage between two adjacent molecules in dimers and short oligomers of glucose. It has been shown that enhanced levels of HjCel3A in H. jecorina cellulase mixtures benefit the conversion of cellulose to glucose. Biochemical characterization of HjCel3A shows that the enzyme efficiently hydrolyzes (1,4)- as well as (1,2)-, (1,3)-, and (1,6)-β-D-linked disaccharides. For crystallization studies, HjCel3A was produced in both H. jecorina (HjCel3A) and Pichia pastoris (Pp-HjCel3A). Whereas the thermostabilities of HjCel3A and Pp-HjCel3A are the same, Pp-HjCel3A has a higher degree of N-linked glycosylation. Here, we present x-ray structures of HjCel3A with and without glucose bound in the active site. The structures have a three-domain architecture as observed previously for other glycoside hydrolase family 3 β-glucosidases. Both production hosts resulted in HjCel3A structures that have N-linked glycosylations at Asn(208) and Asn(310). In H. jecorina-produced HjCel3A, a single N-acetylglucosamine is present at both sites, whereas in Pp-HjCel3A, the P. pastoris-produced HjCel3A enzyme, the glycan chains consist of 8 or 4 saccharides. The glycosylations are involved in intermolecular contacts in the structures derived from either host. Due to the different sizes of the glycosylations, the interactions result in different crystal forms for the two protein forms.


  • Organizational Affiliation

    From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-D-GLUCOSIDE GLUCOHYDROLASE713Trichoderma reeseiMutation(s): 0 
EC: 3.2.1.21
UniProt
Find proteins for Q12715 (Hypocrea jecorina)
Explore Q12715 
Go to UniProtKB:  Q12715
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12715
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.065α = 90
b = 82.404β = 90
c = 136.722γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2014-11-19
    Changes: Database references
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.5: 2024-11-13
    Changes: Data collection, Database references, Structure summary