Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.37 kDa 
• Atom Count: 4256 
• Modelled Residue Count: 477 
• Deposited Residue Count: 499 
• Unique protein chains: 1

4MDP

Crystal structure of a GH1 beta-glucosidase from the fungus Humicola insolens in complex with glucose

• PDB DOI: 10.2210/pdb4MDP/pdb

• Classification: HYDROLASE
• Organism(s): [Humicola] grisea var. thermoidea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-23 Released: 2014-06-25 
• Deposition Author(s): Giuseppe, P.O., Souza, T.A.C.B., Souza, F.H.M., Zanphorlin, L.M., Machado, C.B., Ward, R.J., Jorge, J.A., Furriel, R.P.M., Murakami, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.214 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Structural basis for glucose tolerance in GH1 beta-glucosidases.

Giuseppe, P.O., Souza, T.A.C.B., Souza, F.H.M., Zanphorlin, L.M., Machado, C.B., Ward, R.J., Jorge, J.A., Furriel, R.P.M., Murakami, M.T.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1631-1639

• PubMed: 24914974 
• DOI: 10.1107/S1399004714006920
• Primary Citation of Related Structures:  
  4MDO, 4MDP


• PubMed Abstract: 
  

Product inhibition of β-glucosidases (BGs) by glucose is considered to be a limiting step in enzymatic technologies for plant-biomass saccharification. Remarkably, some β-glucosidases belonging to the GH1 family exhibit unusual properties, being tolerant to, or even stimulated by, high glucose concentrations. However, the structural basis for the glucose tolerance and stimulation of BGs is still elusive. To address this issue, the first crystal structure of a fungal β-glucosidase stimulated by glucose was solved in native and glucose-complexed forms, revealing that the shape and electrostatic properties of the entrance to the active site, including the +2 subsite, determine glucose tolerance. The aromatic Trp168 and the aliphatic Leu173 are conserved in glucose-tolerant GH1 enzymes and contribute to relieving enzyme inhibition by imposing constraints at the +2 subsite that limit the access of glucose to the -1 subsite. The GH1 family β-glucosidases are tenfold to 1000-fold more glucose tolerant than GH3 BGs, and comparative structural analysis shows a clear correlation between active-site accessibility and glucose tolerance. The active site of GH1 BGs is located in a deep and narrow cavity, which is in contrast to the shallow pocket in the GH3 family BGs. These findings shed light on the molecular basis for glucose tolerance and indicate that GH1 BGs are more suitable than GH3 BGs for biotechnological applications involving plant cell-wall saccharification.

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Organizational Affiliation: 

Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, CP 6192, 13083-970 Campinas-SP, Brazil.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A	499	[Humicola] grisea var. thermoidea	Mutation(s): 0  Gene Names: bgl4
UniProt
Find proteins for O93784 (Humicola grisea var. thermoidea) Explore O93784  Go to UniProtKB:  O93784

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
PEG	C [auth A], D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.214 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.567	α = 90
b = 113.567	β = 90
c = 178.74	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-23 
• Released Date: 2014-06-25 
Deposition Author(s): Giuseppe, P.O., Souza, T.A.C.B., Souza, F.H.M., Zanphorlin, L.M., Machado, C.B., Ward, R.J., Jorge, J.A., Furriel, R.P.M., Murakami, M.T.

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2015-07-29
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary