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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.82 kDa 
• Atom Count: 3167 
• Modelled Residue Count: 312 
• Deposited Residue Count: 334 
• Unique protein chains: 1

4N1I

Crystal Structure of the alpha-L-arabinofuranosidase UmAbf62A from Ustilago maidys

• PDB DOI: 10.2210/pdb4N1I/pdb

• Classification: HYDROLASE
• Organism(s): Ustilago maydis 521
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2013-10-04 Released: 2014-01-15 
• Deposition Author(s): Siguier, B., Dumon, C., Mourey, L., Tranier, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.139 
• R-Value Work: 0.114 
• R-Value Observed: 0.115 

Literature

First Structural Insights into alpha-L-Arabinofuranosidases from the Two GH62 Glycoside Hydrolase Subfamilies.

Siguier, B., Haon, M., Nahoum, V., Marcellin, M., Burlet-Schiltz, O., Coutinho, P.M., Henrissat, B., Mourey, L., O'Donohue, M.J., Berrin, J.G., Tranier, S., Dumon, C.

(2014) J Biol Chem 289: 5261-5273

• PubMed: 24394409 
• DOI: 10.1074/jbc.M113.528133
• Primary Citation of Related Structures:  
  4N1I, 4N2R, 4N2Z, 4N4B


• PubMed Abstract: 
  

α-L-arabinofuranosidases are glycoside hydrolases that specifically hydrolyze non-reducing residues from arabinose-containing polysaccharides. In the case of arabinoxylans, which are the main components of hemicellulose, they are part of microbial xylanolytic systems and are necessary for complete breakdown of arabinoxylans. Glycoside hydrolase family 62 (GH62) is currently a small family of α-L-arabinofuranosidases that contains only bacterial and fungal members. Little is known about the GH62 mechanism of action, because only a few members have been biochemically characterized and no three-dimensional structure is available. Here, we present the first crystal structures of two fungal GH62 α-L-arabinofuranosidases from the basidiomycete Ustilago maydis (UmAbf62A) and ascomycete Podospora anserina (PaAbf62A). Both enzymes are able to efficiently remove the α-L-arabinosyl substituents from arabinoxylan. The overall three-dimensional structure of UmAbf62A and PaAbf62A reveals a five-bladed β-propeller fold that confirms their predicted classification into clan GH-F together with GH43 α-L-arabinofuranosidases. Crystallographic structures of the complexes with arabinose and cellotriose reveal the important role of subsites +1 and +2 for sugar binding. Intriguingly, we observed that PaAbf62A was inhibited by cello-oligosaccharides and displayed binding affinity to cellulose although no activity was observed on a range of cellulosic substrates. Bioinformatic analyses showed that UmAbf62A and PaAbf62A belong to two distinct subfamilies within the GH62 family. The results presented here provide a framework to better investigate the structure-function relationships within the GH62 family.

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Organizational Affiliation: 

From the Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-L-arabinofuranosidase UmAbf62A	A	334	Ustilago maydis 521	Mutation(s): 0  Gene Names: UM04309.1 EC: 3.2.1.55

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	H [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
TRS	G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.139 
• R-Value Work: 0.114 
• R-Value Observed: 0.115 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.28	α = 90
b = 65.9	β = 90
c = 68.37	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SHELX	model building
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-04 
• Released Date: 2014-01-15 
Deposition Author(s): Siguier, B., Dumon, C., Mourey, L., Tranier, S.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Database references