Crystal structure of Herbaspirillum huttiense L-arabinose 1-dehydrogenase (NAD bound form)

Experimental Data Snapshot

  • Resolution: 1.36 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

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Crystal structure of L-arabinose 1-dehydrogenase as a short-chain reductase/dehydrogenase protein.

Watanabe, S.Yoshiwara, K.Matsubara, R.Watanabe, Y.

(2022) Biochem Biophys Res Commun 604: 14-21

  • DOI: https://doi.org/10.1016/j.bbrc.2022.03.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    l-Arabinose 1-dehydrogenase (AraDH) catalyzes the NAD(P) + -dependent oxidation of l-arabinose to L-arabinono-1,4-lactone in the non-phosphorylative l-arabinose pathway, and is classified into glucose-fructose oxidoreductase and short-chain dehydrogenase/reductase (SDR). We herein report the crystal structure of a SDR-type AraDH (from Herbaspirillum huttiense) for the first time. The interactions between Asp49 and the 2'- and 3'-hydroxyl groups of NAD + were consistent with strict specificity for NAD + . In a binding model for the substrate, Ser155 and Tyr168, highly conserved in the SDR superfamily, interacted with the C1 and/or C2 hydroxyl(s) of l-arabinose, whereas interactions between Asp107, Arg109, and Gln206 and the C2 and/or C3 hydroxyl(s) were unique to AraDH. Trp200 significantly contributed to the selectivities of the C4 hydroxyl and C6 methyl of substrates.

  • Organizational Affiliation

    Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
A, B
272Herbaspirillum huttiense subsp. putei IAM 15032Mutation(s): 0 
Gene Names: DFS02_4196
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.36 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.509α = 90
b = 83.562β = 113.04
c = 81.927γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description