Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound

Experimental Data Snapshot

  • Resolution: 2.08 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound.

Buer, B.C.Paul, B.Das, D.Stuckey, J.A.Marsh, E.N.

(2014) ACS Chem Biol 9: 2584-2593

  • DOI: https://doi.org/10.1021/cb500343j
  • Primary Citation of Related Structures:  
    4PG0, 4PG1, 4PGI, 4PGK, 4TW3

  • PubMed Abstract: 

    The nonheme diiron enzyme cyanobacterial aldehyde deformylating oxygenase, cADO, catalyzes the highly unusual deformylation of aliphatic aldehydes to alkanes and formate. We have determined crystal structures for the enzyme with a long-chain water-soluble aldehyde and medium-chain carboxylic acid bound to the active site. These structures delineate a hydrophobic channel that connects the solvent with the deeply buried active site and reveal a mode of substrate binding that is different from previously determined structures with long-chain fatty acids bound. The structures also identify a water channel leading to the active site that could facilitate the entry of protons required in the reaction. NMR studies examining 1-[(13)C]-octanal binding to cADO indicate that the enzyme binds the aldehyde form rather than the hydrated form. Lastly, the fortuitous cocrystallization of the metal-free form of the protein with aldehyde bound has revealed protein conformation changes that are involved in binding iron.

  • Organizational Affiliation

    Department of Chemistry, ‡Life Sciences Institute, and §Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde decarbonylase250Prochlorococcus marinus str. MIT 9313Mutation(s): 2 
Gene Names: PMT_1231
Find proteins for Q7V6D4 (Prochlorococcus marinus (strain MIT 9313))
Explore Q7V6D4 
Go to UniProtKB:  Q7V6D4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7V6D4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.08 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.071α = 90
b = 77.071β = 90
c = 117.259γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
Cootmodel building
MD2data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description