4JHL

Crystal Structure of of Axe2, an Acetylxylan Esterase from Geobacillus stearothermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A unique octameric structure of Axe2, an intracellular acetyl-xylooligosaccharide esterase from Geobacillus stearothermophilus.

Lansky, S.Alalouf, O.Solomon, H.V.Alhassid, A.Govada, L.Chayen, N.E.Belrhali, H.Shoham, Y.Shoham, G.

(2014) Acta Crystallogr.,Sect.D 70: 261-278

  • DOI: 10.1107/S139900471302840X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Geobacillus stearothermophilus T6 is a thermophilic, Gram-positive soil bacterium that possesses an extensive and highly regulated hemicellulolytic system, allowing the bacterium to efficiently degrade high-molecular-weight polysaccharides such as xy ...

    Geobacillus stearothermophilus T6 is a thermophilic, Gram-positive soil bacterium that possesses an extensive and highly regulated hemicellulolytic system, allowing the bacterium to efficiently degrade high-molecular-weight polysaccharides such as xylan, arabinan and galactan. As part of the xylan-degradation system, the bacterium uses a number of side-chain-cleaving enzymes, one of which is Axe2, a 219-amino-acid intracellular serine acetylxylan esterase that removes acetyl side groups from xylooligosaccharides. Bioinformatic analyses suggest that Axe2 belongs to the lipase GDSL family and represents a new family of carbohydrate esterases. In the current study, the detailed three-dimensional structure of Axe2 is reported, as determined by X-ray crystallography. The structure of the selenomethionine derivative Axe2-Se was initially determined by single-wavelength anomalous diffraction techniques at 1.70 Å resolution and was used for the structure determination of wild-type Axe2 (Axe2-WT) and the catalytic mutant Axe2-S15A at 1.85 and 1.90 Å resolution, respectively. These structures demonstrate that the three-dimensional structure of the Axe2 monomer generally corresponds to the SGNH hydrolase fold, consisting of five central parallel β-sheets flanked by two layers of helices (eight α-helices and five 310-helices). The catalytic triad residues, Ser15, His194 and Asp191, are lined up along a substrate channel situated on the concave surface of the monomer. Interestingly, the Axe2 monomers are assembled as a `doughnut-shaped' homo-octamer, presenting a unique quaternary structure built of two staggered tetrameric rings. The eight active sites are organized in four closely situated pairs, which face the relatively wide internal cavity. The biological relevance of this octameric structure is supported by independent results obtained from gel-filtration, TEM and SAXS experiments. These data and their comparison to the structural data of related hydrolases are used for a more general discussion focusing on the structure-function relationships of enzymes of this category.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of Axe2, an acetylxylan esterase from Geobacillus stearothermophilus.
      Lansky, S.,Alalouf, O.,Solomon, V.,Alhassid, A.,Govada, L.,Chayan, N.E.,Belrhali, H.,Shoham, Y.,Shoham, G.
      (2013) Acta Crystallogr.,Sect.F 69: 430


    Organizational Affiliation

    Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetyl xylan esterase
A, B
219Geobacillus stearothermophilusMutation(s): 0 
Gene Names: axe2
EC: 3.1.1.72
Find proteins for Q09LX1 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q09LX1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.131 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 110.301α = 90.00
b = 110.301β = 90.00
c = 213.088γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
PHENIXphasing
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references