P. syringae AldA Indole-3-Acetaldehyde Dehydrogenase C302A mutant in complex with NAD+ and IAA

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

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Investigating the reaction and substrate preference of indole-3-acetaldehyde dehydrogenase from the plant pathogen Pseudomonas syringae PtoDC3000.

Zhang, K.Lee, J.S.Liu, R.Chan, Z.T.Dawson, T.J.De Togni, E.S.Edwards, C.T.Eng, I.K.Gao, A.R.Goicouria, L.A.Hall, E.M.Hu, K.A.Huang, K.Kizhner, A.Kodama, K.C.Lin, A.Z.Liu, J.Y.Lu, A.Y.Peng, O.W.Ryu, E.P.Shi, S.Sorkin, M.L.Walker, P.L.Wang, G.J.Xu, M.C.Yang, R.S.Cascella, B.Cruz, W.Holland, C.K.McClerkin, S.A.Kunkel, B.N.Lee, S.G.Jez, J.M.

(2020) Biosci Rep 40

  • DOI: https://doi.org/10.1042/BSR20202959
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aldehyde dehydrogenases (ALDHs) catalyze the conversion of various aliphatic and aromatic aldehydes into corresponding carboxylic acids. Traditionally considered as housekeeping enzymes, new biochemical roles are being identified for members of ALDH family. Recent work showed that AldA from the plant pathogen Pseudomonas syringae strain PtoDC3000 (PtoDC3000) functions as an indole-3-acetaldehyde dehydrogenase for the synthesis of indole-3-acetic acid (IAA). IAA produced by AldA allows the pathogen to suppress salicylic acid-mediated defenses in the model plant Arabidopsis thaliana. Here we present a biochemical and structural analysis of the AldA indole-3-acetaldehyde dehydrogenase from PtoDC3000. Site-directed mutants targeting the catalytic residues Cys302 and Glu267 resulted in a loss of enzymatic activity. The X-ray crystal structure of the catalytically inactive AldA C302A mutant in complex with IAA and NAD+ showed the cofactor adopting a conformation that differs from the previously reported structure of AldA. These structures suggest that NAD+ undergoes a conformational change during the AldA reaction mechanism similar to that reported for human ALDH. Site-directed mutagenesis of the IAA binding site indicates that changes in the active site surface reduces AldA activity; however, substitution of Phe169 with a tryptophan altered the substrate selectivity of the mutant to prefer octanal. The present study highlights the inherent biochemical versatility of members of the ALDH enzyme superfamily in P. syringae.

  • Organizational Affiliation

    Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, U.S.A.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase family protein
A, B, C, D, E
A, B, C, D, E, F, G, H
497Pseudomonas syringae pv. tomato str. DC3000Mutation(s): 1 
Gene Names: PSPTO_0092
Find proteins for Q88BC5 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000))
Explore Q88BC5 
Go to UniProtKB:  Q88BC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88BC5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAI

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
C21 H29 N7 O14 P2
Query on IAC

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
C10 H9 N O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 333.816α = 90
b = 161.095β = 90.01
c = 84.999γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2021-06-23 
  • Deposition Author(s): Jez, J.M.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1614539
National Science Foundation (NSF, United States)United StatesIOS-1645908
National Science Foundation (NSF, United States)United StatesDGE-1143954
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description