4PGI

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

Summary for 4PGI

• Entry DOI: 10.2210/pdb4pgi/pdb
• Related: 4PG0 4PG1
• Descriptor: Aldehyde decarbonylase, FE (III) ION, 11-[2-(2-ethoxyethoxy)ethoxy]undecanal, ... (5 entities in total)
• Functional Keywords: non-heme di-iron protein, hydrocarbon production, alpha-helix, lyase, oxidoreductase
• Biological source: Prochlorococcus marinus
• Total number of polymer chains: 1
• Total formula weight: 28528.06

Authors

Buer, B.C.,Paul, B.,Das, D.,Stuckey, J.A.,Marsh, E.N.G. (deposition date: 2014-05-02, release date: 2015-02-11, Last modification date: 2023-09-27)

Primary citation

Buer, B.C.,Paul, B.,Das, D.,Stuckey, J.A.,Marsh, E.N.
Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound.
Acs Chem.Biol., 9:2584-2593, 2014

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.

PubMed: 25222710
DOI: 10.1021/cb500343j

Experimental method

X-RAY DIFFRACTION (2.08 Å)