7DB5

Crystal structure of alpha-L-fucosidase from Vibrio sp. strain EJY3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dual alpha-1,4- and beta-1,4-Glycosidase Activities by the Novel Carbohydrate-Binding Module in alpha-l-Fucosidase from Vibrio sp. Strain EJY3.

Hong, H.Kim, D.H.Seo, H.Kim, K.H.Kim, K.J.

(2021) J Agric Food Chem 69: 3380-3389

  • DOI: 10.1021/acs.jafc.0c08199
  • Primary Citation of Related Structures:  
    7DB5

  • PubMed Abstract: 
  • Carbohydrates are structurally and functionally diverse materials including polysaccharides, and marine organisms are known to have many enzymes for the breakdown of complex polysaccharides. Here, we identified an α-l-fucosidase enzyme from the marine bacterium Vibrio sp ...

    Carbohydrates are structurally and functionally diverse materials including polysaccharides, and marine organisms are known to have many enzymes for the breakdown of complex polysaccharides. Here, we identified an α-l-fucosidase enzyme from the marine bacterium Vibrio sp. strain EJY3 ( Vej FCD) that has dual α-1,4-glucosidic and β-1,4-galactosidic specificities. We determined the crystal structure of Vej FCD and provided the structural basis underlying the dual α- and β-glycosidase activities of the enzyme. Unlike other three-domain FCDs, in Vej FCD, carbohydrate-binding module-B (CBM-B) with a novel β-sandwich fold tightly contacts with the CatD/CBM-B main body and provides key residues for the β-1,4-glycosidase activity of the enzyme. The phylogenetic tree analysis suggests that only a few FCDs from marine microorganisms have the key structural features for dual α-1,4- and β-1,4-glycosidase activities. This study provides the structural insights into the mechanism underlying the novel glycoside hydrolase activities and could be applied for more efficient utilization in the hydrolysis of complex carbohydrates in biotechnological applications.


    Organizational Affiliation

    KNU Institute of Microbiology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 41566, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-L-fucosidaseA616Vibrio sp. EJY3Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.916α = 90
b = 163.916β = 90
c = 58.712γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2020-10-19 
  • Released Date: 2021-03-24 
  • Deposition Author(s): Hong, H., Kim, K.-J.

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references