2J3J

Crystal structure of Arabidopsis thaliana Double Bond Reductase (AT5G16970)-Ternary Complex I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.055 
  • R-Value Observed: 0.055 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanistic and structural studies of apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase At5g16970.

Youn, B.Kim, S.J.Moinuddin, S.G.Lee, C.Bedgar, D.L.Harper, A.R.Davin, L.B.Lewis, N.G.Kang, C.

(2006) J Biol Chem 281: 40076-40088

  • DOI: https://doi.org/10.1074/jbc.M605900200
  • Primary Citation of Related Structures:  
    2J3H, 2J3I, 2J3J, 2J3K

  • PubMed Abstract: 

    In this study, we determined the crystal structures of the apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase encoded by At5g16970. This protein, one of 11 homologues in Arabidopsis thaliana, is most closely related to the Pinus taeda phenylpropenal double bond reductase, involved in, for example, heartwood formation. Both enzymes also have essential roles in plant defense, and can function by catalyzing the reduction of the 7-8-double bond of phenylpropanal substrates, such as p-coumaryl and coniferyl aldehydes in vitro. At5g16970 is also capable of reducing toxic substrates with the same alkenal functionality, such as 4-hydroxy-(2E)-nonenal. The overall fold of At5g16970 is similar to that of the zinc-independent medium chain dehydrogenase/reductase superfamily, the members of which have two domains and are dimeric in nature, i.e. in contrast to their original classification as being zinc-containing oxidoreductases. As provisionally anticipated from the kinetic data, the shape of the binding pocket can readily accommodate p-coumaryl aldehyde, coniferyl aldehyde, 4-hydroxy-(2E)-nonenal, and 2-alkenals. However, the enzyme kinetic data among these potential substrates differ, favoring p-coumaryl aldehyde. Tyr-260 is provisionally proposed to function as a general acid/base for hydride transfer. A catalytic mechanism for this reduction, and its applicability to related important detoxification mammalian proteins, is also proposed.


  • Organizational Affiliation

    School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADPH-dependent oxidoreductase 2-alkenal reductase
A, B
345Arabidopsis thalianaMutation(s): 0 
Gene Names: AERP1At5g16970F2K13_120
EC: 1.3.1 (PDB Primary Data), 1.3.1.74 (PDB Primary Data)
UniProt
Find proteins for Q39172 (Arabidopsis thaliana)
Explore Q39172 
Go to UniProtKB:  Q39172
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39172
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
HC4
Query on HC4

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
4'-HYDROXYCINNAMIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.055 
  • R-Value Observed: 0.055 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.04α = 90
b = 122.54β = 90
c = 147.65γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-12-05
    Changes: Data collection, Database references, Source and taxonomy, Structure summary