1ODU

CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE IN COMPLEX WITH FUCOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Thermotoga Maritima {Alpha}-L-Fucosidase: Insights Into the Catalytic Mechanism and the Molecular Basis for Fucosidosis

Sulzenbacher, G.Bignon, C.Nishimura, T.Tarling, C.Withers, S.Henrissat, B.Bourne, Y.

(2004) J Biol Chem 279: 13119

  • DOI: 10.1074/jbc.M313783200
  • Primary Citation of Related Structures:  
    1HL8, 1HL9, 1ODU

  • PubMed Abstract: 
  • Fucosylated glycoconjugates are involved in numerous biological events, and alpha-l-fucosidases, the enzymes responsible for their processing, are therefore of crucial importance. Deficiency in alpha-l-fucosidase activity is associated with fucosidosis, a lysosomal storage disorder characterized by rapid neurodegeneration, resulting in severe mental and motor deterioration ...

    Fucosylated glycoconjugates are involved in numerous biological events, and alpha-l-fucosidases, the enzymes responsible for their processing, are therefore of crucial importance. Deficiency in alpha-l-fucosidase activity is associated with fucosidosis, a lysosomal storage disorder characterized by rapid neurodegeneration, resulting in severe mental and motor deterioration. To gain insight into alpha-l-fucosidase function at the molecular level, we have determined the crystal structure of Thermotoga maritima alpha-l-fucosidase. This enzyme assembles as a hexamer and displays a two-domain fold, composed of a catalytic (beta/alpha)(8)-like domain and a C-terminal beta-sandwich domain. The structures of an enzyme-product complex and of a covalent glycosyl-enzyme intermediate, coupled with kinetic and mutagenesis studies, allowed us to identify the catalytic nucleophile, Asp(244), and the Brønsted acid/base, Glu(266). Because T. maritima alpha-l-fucosidase occupies a unique evolutionary position, being far more closely related to the mammalian enzymes than to any other prokaryotic homolog, a structural model of the human enzyme was built to document the structural consequences of the genetic mutations associated with fucosidosis.


    Related Citations: 
    • Identification of the Catalytic Nucleophile of the Family 29 Alpha -L-Fucosidase from Thermotoga Maritima Through Trapping of a Covalent Glycosyl-Enzyme Intermediate and Mutagenesis
      Tarling, C., He, S., Sulzenbacher, G., Bignon, C., Bourne, Y., Henrissat, B., Withers, S.
      (2003) J Biol Chem 278: 47394

    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS, and Universités Aix-Marseille I and II, 31 Chemin J. Aiguier, F-13402 Marseille Cedex 20, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE ALPHA-L-FUCOSIDASEA, B449Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: TM_0306
EC: 3.2.1.51
UniProt
Find proteins for Q9WYE2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WYE2 
Go to UniProtKB:  Q9WYE2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYE2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUL
Query on FUL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
beta-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.08α = 90
b = 179.08β = 90
c = 174.692γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary