6GN6

Alpha-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Active site complementation and hexameric arrangement in the GH family 29; a structure-function study of alpha-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus.

Kovalova, T.Koval, T.Benesova, E.Vodickova, P.Spiwok, V.Lipovova, P.Dohnalek, J.

(2019) Glycobiology 29: 59-73

  • DOI: 10.1093/glycob/cwy078

  • PubMed Abstract: 
  • α-l-Fucosidase isoenzyme 1 from bacterium Paenibacillus thiaminolyticus is a member of the glycoside hydrolase family GH29 capable of cleaving l-fucose from nonreducing termini of oligosaccharides and glycoconjugates. Here we present the first crysta ...

    α-l-Fucosidase isoenzyme 1 from bacterium Paenibacillus thiaminolyticus is a member of the glycoside hydrolase family GH29 capable of cleaving l-fucose from nonreducing termini of oligosaccharides and glycoconjugates. Here we present the first crystal structure of this protein revealing a novel quaternary state within this family. The protein is in a unique hexameric assembly revealing the first observed case of active site complementation by a residue from an adjacent monomer in this family. Mutation of the complementing tryptophan residue caused changes in the catalytic properties including a shift of the pH optimum, a change of affinity to an artificial chromogenic substrate and a decreased reaction rate for a natural substrate. The wild-type enzyme was active on most of the tested naturally occurring oligosaccharides and capable of transglycosylation on a variety of acceptor molecules, including saccharides, alcohols or chromogenic substrates. Mutation of the complementing residue changed neither substrate specificity nor the preference for the type of transglycosylation acceptor molecule; however, the yields of the reactions were lower in both cases. Maltose molecules bound to the enzyme in the crystal structure identified surface carbohydrate-binding sites, possibly participating in binding of larger oligosaccharides.


    Organizational Affiliation

    Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v.v.i., Biocev, Vestec, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-L-fucosidase
A, B, C, D, E, F
447Paenibacillus thiaminolyticusMutation(s): 0 
Gene Names: aLfuk1
EC: 3.2.1.51
Find proteins for E3PQQ9 (Paenibacillus thiaminolyticus)
Go to UniProtKB:  E3PQQ9
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

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Download CCD File 
A, E, F
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
NA
Query on NA

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C, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

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Download CCD File 
A, B, C, D, E, F
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

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C, E
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A, B, C, D, E, F
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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B, F
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 107.772α = 90.00
b = 148.758β = 90.00
c = 194.895γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionCzech RepublicCZ.02.1.01/0.0/0.0/16_013/0001776
European CommissionCzech RepublicCZ.1.05/1.1.00/02.0109
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2015043

Revision History 

  • Version 1.0: 2018-12-26
    Type: Initial release