Structure of the aminoaldehyde dehydrogenase 1 E260A mutant from Solanum lycopersicum (SlAMADH1-E260A)

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

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Plant ALDH10 family: identifying critical residues for substrate specificity and trapping a thiohemiacetal intermediate.

Kopecny, D.Koncitikova, R.Tylichova, M.Vigouroux, A.Moskalikova, H.Soural, M.Sebela, M.Morera, S.

(2013) J Biol Chem 288: 9491-9507

  • DOI: https://doi.org/10.1074/jbc.M112.443952
  • Primary Citation of Related Structures:  
    4I8P, 4I8Q, 4I9B

  • PubMed Abstract: 

    Plant ALDH10 family members are aminoaldehyde dehydrogenases (AMADHs), which oxidize ω-aminoaldehydes to the corresponding acids. They have been linked to polyamine catabolism, osmoprotection, secondary metabolism (fragrance), and carnitine biosynthesis. Plants commonly contain two AMADH isoenzymes. We previously studied the substrate specificity of two AMADH isoforms from peas (PsAMADHs). Here, two isoenzymes from tomato (Solanum lycopersicum), SlAMADHs, and three AMADHs from maize (Zea mays), ZmAMADHs, were kinetically investigated to obtain further clues to the catalytic mechanism and the substrate specificity. We also solved the high resolution crystal structures of SlAMADH1 and ZmAMADH1a because these enzymes stand out from the others regarding their activity. From the structural and kinetic analysis, we can state that five residues at positions 163, 288, 289, 444, and 454 (PsAMADHs numbering) can, directly or not, significantly modulate AMADH substrate specificity. In the SlAMADH1 structure, a PEG aldehyde derived from the precipitant forms a thiohemiacetal intermediate, never observed so far. Its absence in the SlAMADH1-E260A structure suggests that Glu-260 can activate the catalytic cysteine as a nucleophile. We show that the five AMADHs studied here are capable of oxidizing 3-dimethylsulfoniopropionaldehyde to the cryo- and osmoprotectant 3-dimethylsulfoniopropionate. For the first time, we also show that 3-acetamidopropionaldehyde, the third aminoaldehyde besides 3-aminopropionaldehyde and 4-aminobutyraldehyde, is generally oxidized by AMADHs, meaning that these enzymes are unique in metabolizing and detoxifying aldehyde products of polyamine degradation to nontoxic amino acids. Finally, gene expression profiles in maize indicate that AMADHs might be important for controlling ω-aminoaldehyde levels during early stages of the seed development.

  • Organizational Affiliation

    Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic. kopecny_david@yahoo.co.uk

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative betaine aldehyde dehyrogenase514Solanum lycopersicumMutation(s): 1 
Gene Names: Solyc06g071290.2
Find proteins for Q56R04 (Solanum lycopersicum)
Explore Q56R04 
Go to UniProtKB:  Q56R04
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56R04
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
C21 H27 N7 O14 P2
Query on PEG

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H [auth A],
K [auth A],
L [auth A]
C4 H10 O3
Query on EDO

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C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth A],
J [auth A]
C2 H6 O2
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.04α = 90
b = 118.07β = 90
c = 128.21γ = 90
Software Package:
Software NamePurpose
PX1data collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2014-01-01
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description