Crystal structure of aminoaldehyde dehydrogenase 1 from Pisum sativum (PsAMADH1)

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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Structural and functional characterization of plant aminoaldehyde dehydrogenase from Pisum sativum with a broad specificity for natural and synthetic aminoaldehydes.

Tylichova, M.Kopecny, D.Morera, S.Briozzo, P.Lenobel, R.Snegaroff, J.Sebela, M.

(2010) J Mol Biol 396: 870-882

  • DOI: https://doi.org/10.1016/j.jmb.2009.12.015
  • Primary Citation of Related Structures:  
    3IWJ, 3IWK

  • PubMed Abstract: 

    Aminoaldehyde dehydrogenases (AMADHs, EC belong to the large aldehyde dehydrogenase (ALDH) superfamily, namely, the ALDH9 family. They oxidize polyamine-derived omega-aminoaldehydes to the corresponding omega-amino acids. Here, we report the first X-ray structures of plant AMADHs: two isoenzymes, PsAMADH1 and PsAMADH2, from Pisum sativum in complex with beta-nicotinamide adenine dinucleotide (NAD(+)) at 2.4 and 2.15 A resolution, respectively. Both recombinant proteins are dimeric and, similarly to other ALDHs, each monomer is composed of an oligomerization domain, a coenzyme binding domain and a catalytic domain. Each subunit binds NAD(+) as a coenzyme, contains a solvent-accessible C-terminal peroxisomal targeting signal (type 1) and a cation bound in the cavity close to the NAD(+) binding site. While the NAD(+) binding mode is classical for PsAMADH2, that for PsAMADH1 is unusual among ALDHs. A glycerol molecule occupies the substrate binding site and mimics a bound substrate. Structural analysis and substrate specificity study of both isoenzymes in combination with data published previously on other ALDH9 family members show that the established categorization of such enzymes into distinct groups based on substrate specificity is no more appropriate, because many of them seem capable of oxidizing a large spectrum of aminoaldehyde substrates. PsAMADH1 and PsAMADH2 can oxidize N,N,N-trimethyl-4-aminobutyraldehyde into gamma-butyrobetaine, which is the carnitine precursor in animal cells. This activity highly suggests that in addition to their contribution to the formation of compatible osmolytes such as glycine betaine, beta-alanine betaine and gamma-aminobutyric acid, AMADHs might participate in carnitine biosynthesis in plants.

  • Organizational Affiliation

    Department of Biochemistry, Faculty of Science, Palacký University, Slechtitelů 11, CZ-783 71 Olomouc, Czech Republic.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoaldehyde dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
503Pisum sativumMutation(s): 0 
Gene Names: amadh1
Find proteins for Q8VWZ1 (Pisum sativum)
Explore Q8VWZ1 
Go to UniProtKB:  Q8VWZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VWZ1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth G]
JA [auth H]
MA [auth I]
N [auth A]
BA [auth F],
EA [auth G],
JA [auth H],
MA [auth I],
N [auth A],
P [auth B],
PA [auth J],
T [auth C],
TA [auth K],
W [auth D],
YA [auth L],
Z [auth E]
C21 H27 N7 O14 P2
Query on MRD

Download Ideal Coordinates CCD File 
C6 H14 O2
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth L]
BB [auth L]
CA [auth F]
CB [auth L]
DB [auth L]
AB [auth L],
BB [auth L],
CA [auth F],
CB [auth L],
DB [auth L],
FA [auth G],
GA [auth G],
HA [auth G],
KA [auth H],
NA [auth I],
Q [auth B],
QA [auth J],
R [auth B],
RA [auth J],
U [auth C],
UA [auth K],
VA [auth K],
WA [auth K],
ZA [auth L]
C3 H8 O3
Query on NA

Download Ideal Coordinates CCD File 
AA [auth F]
DA [auth G]
IA [auth H]
LA [auth I]
M [auth A]
AA [auth F],
DA [auth G],
IA [auth H],
LA [auth I],
M [auth A],
O [auth B],
OA [auth J],
S [auth C],
SA [auth K],
V [auth D],
XA [auth L],
Y [auth E]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.41α = 90
b = 216.87β = 98.02
c = 205.76γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-12-04
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description