6X9L

Crystal Structure of Aldehyde Dehydrogenase C (AldC) mutant (C291A) from Pseudomonas syringae in complexed with NAD+ and Octanal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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This is version 1.3 of the entry. See complete history


Literature

The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase.

Lee, S.G.Harline, K.Abar, O.Akadri, S.O.Bastian, A.G.Chen, H.S.Duan, M.Focht, C.M.Groziak, A.R.Kao, J.Kottapalli, J.S.Leong, M.C.Lin, J.J.Liu, R.Luo, J.E.Meyer, C.M.Mo, A.F.Pahng, S.H.Penna, V.Raciti, C.D.Srinath, A.Sudhakar, S.Tang, J.D.Cox, B.R.Holland, C.K.Cascella, B.Cruz, W.McClerkin, S.A.Kunkel, B.N.Jez, J.M.

(2020) J Biol Chem 295: 13914-13926

  • DOI: https://doi.org/10.1074/jbc.RA120.014747

  • PubMed Abstract: 

    Aldehyde dehydrogenases are versatile enzymes that serve a range of biochemical functions. Although traditionally considered metabolic housekeeping enzymes because of their ability to detoxify reactive aldehydes, like those generated from lipid peroxidation damage, the contributions of these enzymes to other biological processes are widespread. For example, the plant pathogen Pseudomonas syringae strain Pto DC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. Here we investigate the biochemical function of AldC from Pto DC3000. Analysis of the substrate profile of AldC suggests that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. The 2.5 Å resolution X-ray crystal of the AldC C291A mutant in a dead-end complex with octanal and NAD + reveals an apolar binding site primed for aliphatic aldehyde substrate recognition. Functional characterization of site-directed mutants targeting the substrate- and NAD(H)-binding sites identifies key residues in the active site for ligand interactions, including those in the "aromatic box" that define the aldehyde-binding site. Overall, this study provides molecular insight for understanding the evolution of the prokaryotic aldehyde dehydrogenase superfamily and their diversity of function.


  • Organizational Affiliation

    Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, North Carolina, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase family protein
A, B
491Pseudomonas syringae pv. tomato str. DC3000Mutation(s): 1 
Gene Names: PSPTO_3644
UniProt
Find proteins for Q87YZ5 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000))
Explore Q87YZ5 
Go to UniProtKB:  Q87YZ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87YZ5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.193α = 90
b = 92.17β = 90
c = 231.357γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PHASERphasing
Cootmodel building
HKL-3000data scaling
HKL-3000data collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNIH-AI-097119

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-10-14
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description