2XVL

crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with Pentaerythritol propoxylate (5 4 PO OH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Enzymatic Characterisation of a Glycoside Hydrolase Family 31 Alpha-Xylosidase from Cellvibrio Japonicus Involved in Xyloglucan Saccharification.

Larsbrink, J.Izumi, A.Ibatullin, F.Nakhai, A.Gilbert, H.J.Davies, G.J.Brumer, H.

(2011) Biochem.J. 436: 567

  • DOI: 10.1042/BJ20110299
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The desire for improved methods of biomass conversion into fuels and feedstocks has re-awakened interest in the enzymology of plant cell wall degradation. The complex polysaccharide xyloglucan is abundant in plant matter, where it may account for up ...

    The desire for improved methods of biomass conversion into fuels and feedstocks has re-awakened interest in the enzymology of plant cell wall degradation. The complex polysaccharide xyloglucan is abundant in plant matter, where it may account for up to 20% of the total primary cell wall carbohydrates. Despite this, few studies have focused on xyloglucan saccharification, which requires a consortium of enzymes including endo-xyloglucanases, α-xylosidases, β-galactosidases and α-L-fucosidases, among others. In the present paper, we show the characterization of Xyl31A, a key α-xylosidase in xyloglucan utilization by the model Gram-negative soil saprophyte Cellvibrio japonicus. CjXyl31A exhibits high regiospecificity for the hydrolysis of XGOs (xylogluco-oligosaccharides), with a particular preference for longer substrates. Crystallographic structures of both the apo enzyme and the trapped covalent 5-fluoro-β-xylosyl-enzyme intermediate, together with docking studies with the XXXG heptasaccharide, revealed, for the first time in GH31 (glycoside hydrolase family 31), the importance of a PA14 domain insert in the recognition of longer oligosaccharides by extension of the active-site pocket. The observation that CjXyl31A was localized to the outer membrane provided support for a biological model of xyloglucan utilization by C. japonicus, in which XGOs generated by the action of a secreted endo-xyloglucanase are ultimately degraded in close proximity to the cell surface. Moreover, the present study diversifies the toolbox of glycosidases for the specific modification and saccharification of cell wall polymers for biotechnological applications.


    Organizational Affiliation

    Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-XYLOSIDASE, PUTATIVE, XYL31A
A
1020Cellvibrio japonicus (strain Ueda107)Mutation(s): 0 
Gene Names: xyl31A
EC: 3.2.1.-
Find proteins for B3PBD9 (Cellvibrio japonicus (strain Ueda107))
Go to UniProtKB:  B3PBD9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
PXN
Query on PXN

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Download CCD File 
A
(2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol
PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)
C17 H36 O8
GXEZGLLPFFKHGE-FPCVCCKLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.145 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 157.653α = 90.00
b = 157.653β = 90.00
c = 226.688γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
BALBESphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-13
    Type: Initial release
  • Version 1.1: 2011-06-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance