2E40

Crystal structure of intracellular family 1 beta-glucosidase BGL1A from the basidiomycete Phanerochaete chrysosporium in complex with gluconolactone

• PDB DOI: https://doi.org/10.2210/pdb2E40/pdb

• Classification: HYDROLASE
• Organism(s): Phanerodontia chrysosporium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-12-01 Released: 2007-03-27 
• Deposition Author(s): Nijikken, Y., Tsukada, T., Igarashi, K., Samejima, M., Fushinobu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.191 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

Crystal structure of intracellular family 1 beta-glucosidase BGL1A from the basidiomycete Phanerochaete chrysosporium

Nijikken, Y., Tsukada, T., Igarashi, K., Samejima, M., Wakagi, T., Shoun, H., Fushinobu, S.

(2007) FEBS Lett 581: 1514-1520

• PubMed: 17376440 
• DOI: https://doi.org/10.1016/j.febslet.2007.03.009
• Primary Citation of Related Structures:  
  2E3Z, 2E40


• PubMed Abstract: 
  

  The white-rot fungus Phanerochaete chrysosporium has two intracellular beta-glucosidases (BGL1A and BGL1B) belonging to glycoside hydrolase (GH) family 1. BGL1B effectively hydrolyzes cellobiose and cellobionolactone, but BGL1A does not. We have determined the crystal structure of BGL1A in substrate-free and gluconolactone complexed forms. The overall structure and the characteristic of subsite -1 (glycone site) were similar to those of other known GH1 enzymes. The loop regions covering on the (beta/alpha)(8) barrel was significantly deviated, and they form a unique subsite +1 (aglycone site) of BGL1A.

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Organizational Affiliation: 

Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Tokyo 113-8657, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 106.27 kDa 
• Atom Count: 8,369 
• Modelled Residue Count: 918 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A, B	465	Phanerodontia chrysosporium	Mutation(s): 0  Gene Names: bgl1A EC: 3.2.1.21
UniProt
Find proteins for Q25BW5 (Phanerodontia chrysosporium) Explore Q25BW5  Go to UniProtKB:  Q25BW5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LGC	C [auth A], D [auth B]	D-glucono-1,5-lactone C6 H10 O6 PHOQVHQSTUBQQK-SQOUGZDYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.191 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.789	α = 90
b = 120.081	β = 90
c = 133.041	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Nijikken, Y., Tsukada, T., Igarashi, K., Samejima, M., Fushinobu, S.

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary