Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (apo-form)

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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This is version 1.3 of the entry. See complete history


Structural insights into the catalytic and substrate recognition mechanisms of bacterial l-arabinose 1-dehydrogenase.

Watanabe, Y.Iga, C.Watanabe, Y.Watanabe, S.

(2019) FEBS Lett 593: 1257-1266

  • DOI: https://doi.org/10.1002/1873-3468.13424
  • Primary Citation of Related Structures:  
    6JNJ, 6JNK

  • PubMed Abstract: 

    In Azospirillum brasilense, a gram-negative nitrogen-fixing bacterium, l-arabinose is converted to α-ketoglutarate through a nonphosphorylative metabolic pathway. In the first step in the pathway, l-arabinose is oxidized to l-arabino-γ-lactone by NAD(P)-dependent l-arabinose 1-dehydrogenase (AraDH) belonging to the glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Here, we determined the crystal structures of apo- and NADP-bound AraDH at 1.5 and 2.2 Å resolutions, respectively. A docking model of l-arabinose and NADP-bound AraDH and structure-based mutational analyses suggest that Lys91 or Asp169 serves as a catalytic base and that Glu147, His153, and Asn173 are responsible for substrate recognition. In particular, Asn173 may play a role in the discrimination between l-arabinose and d-xylose, the C4 epimer of l-arabinose.

  • Organizational Affiliation

    Faculty of Agriculture, Ehime University, Matsuyama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-arabinose 1-dehydrogenase (NAD(P)(+))
A, B
311Azospirillum brasilenseMutation(s): 0 
Gene Names: araA
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Find proteins for Q53TZ2 (Azospirillum brasilense)
Explore Q53TZ2 
Go to UniProtKB:  Q53TZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53TZ2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.7α = 107.77
b = 63.47β = 100.7
c = 66.17γ = 115.98
Software Package:
Software NamePurpose
XDSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-26
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description