4NI3

Crystal Structure of GH29 family alpha-L-fucosidase from Fusarium graminearum in the closed form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 

wwPDB Validation 3D Report Full Report



Literature

Structure and Substrate Specificity of a Eukaryotic Fucosidase from Fusarium graminearum.

Cao, H.Walton, J.D.Brumm, P.Phillips, G.N.

(2014) J Biol Chem 289: 25624-25638

  • DOI: 10.1074/jbc.M114.583286
  • Primary Citation of Related Structures:  
    4NI3, 4PSP, 4PSR

  • PubMed Abstract: 
  • The secreted glycoside hydrolase family 29 (GH29) α-L-fucosidase from plant pathogenic fungus Fusarium graminearum (FgFCO1) actively releases fucose from the xyloglucan fragment. We solved crystal structures of two active-site conformations, i.e. ope ...

    The secreted glycoside hydrolase family 29 (GH29) α-L-fucosidase from plant pathogenic fungus Fusarium graminearum (FgFCO1) actively releases fucose from the xyloglucan fragment. We solved crystal structures of two active-site conformations, i.e. open and closed, of apoFgFCO1 and an open complex with product fucose at atomic resolution. The closed conformation supports catalysis by orienting the conserved general acid/base Glu-288 nearest the predicted glycosidic position, whereas the open conformation possibly represents an unreactive state with Glu-288 positioned away from the catalytic center. A flexible loop near the substrate binding site containing a non-conserved GGSFT sequence is ordered in the closed but not the open form. We also identified a novel C-terminal βγ-crystallin domain in FgFCO1 devoid of calcium binding motif whose homologous sequences are present in various glycoside hydrolase families. N-Glycosylated FgFCO1 adopts a monomeric state as verified by solution small angle x-ray scattering in contrast to reported multimeric fucosidases. Steady-state kinetics shows that FgFCO1 prefers α1,2 over α1,3/4 linkages and displays minimal activity with p-nitrophenyl fucoside with an acidic pH optimum of 4.6. Despite a retaining GH29 family fold, the overall specificity of FgFCO1 most closely resembles inverting GH95 α-fucosidase, which displays the highest specificity with two natural substrates harboring the Fucα1-2Gal glycosidic linkage, a xyloglucan-derived nonasaccharide, and 2'-fucosyllactose. Furthermore, FgFCO1 hydrolyzes H-disaccharide (lacking a +2 subsite sugar) at a rate 10(3)-fold slower than 2'-fucosyllactose. We demonstrated the structurally dynamic active site of FgFCO1 with flexible general acid/base Glu, a common feature shared by several bacterial GH29 fucosidases to various extents.


    Organizational Affiliation

    From Rice University, Houston Texas 77005, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, georgep@rice.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-fucosidase GH29A, B585Fusarium graminearumMutation(s): 0 
Gene Names: FCO1
EC: 3.2.1.51
Find proteins for J9UN47 (Gibberella zeae)
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Go to UniProtKB:  J9UN47
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
6 N-Glycosylation
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TRS
Query on TRS

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A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.145 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.511α = 105.61
b = 75.512β = 107.19
c = 80.367γ = 106.71
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-09-03
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary