1GYD

Structure of Cellvibrio cellulosa alpha-L-arabinanase

• PDB DOI: https://doi.org/10.2210/pdb1GYD/pdb

• Classification: ARABINANASE
• Organism(s): Cellvibrio japonicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-04-23 Released: 2002-08-23 
• Deposition Author(s): Nurizzo, D., Turkenburg, J.P., Charnock, S.J., Roberts, S.M., Dodson, E.J., McKie, V.A., Taylor, E.J., Gilbert, H.J., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.245 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold.

Nurizzo, D., Turkenburg, J.P., Charnock, S.J., Roberts, S.M., Dodson, E.J., McKie, V.A., Taylor, E.J., Gilbert, H.J., Davies, G.J.

(2002) Nat Struct Biol 9: 665-668

• PubMed: 12198486 
• DOI: https://doi.org/10.1038/nsb835
• Primary Citation of Related Structures:  
  1GYD, 1GYE, 1GYH


• PubMed Abstract: 
  

  Cellvibrio japonicus arabinanase Arb43A hydrolyzes the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The three-dimensional structure of Arb43A, determined at 1.9 A resolution, reveals a five-bladed beta-propeller fold. Arb43A is the first enzyme known to display this topology. A long V-shaped surface groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. Three carboxylates deep in the active site groove provide the general acid and base components for glycosidic bond hydrolysis with inversion of anomeric configuration.

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Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 35.93 kDa 
• Atom Count: 2,754 
• Modelled Residue Count: 315 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A	A [auth B]	315	Cellvibrio japonicus	Mutation(s): 0  EC: 3.2.1.99
UniProt
Find proteins for P95470 (Cellvibrio japonicus (strain Ueda107)) Explore P95470  Go to UniProtKB:  P95470

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.245 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.078	α = 90
b = 90.078	β = 90
c = 177.217	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-23 
Deposition Author(s): Nurizzo, D., Turkenburg, J.P., Charnock, S.J., Roberts, S.M., Dodson, E.J., McKie, V.A., Taylor, E.J., Gilbert, H.J., Davies, G.J.

Revision History  

• Version 1.0: 2002-08-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-02-28
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Other, Refinement description