4I3T

Structure of phosphonoacetaldehyde dehydrogenase in the apo state

Summary for 4I3T

• Entry DOI: 10.2210/pdb4i3t/pdb
• Related: 4I3U 4I3V 4I3W 4I3X
• Descriptor: Aldehyde dehydrogenase (NAD+), PHOSPHATE ION (3 entities in total)
• Functional Keywords: aldehyde dehydrogenase, phosphonate catabolism, oxidoreductase
• Biological source: Sinorhizobium meliloti (Ensifer meliloti)
• Total number of polymer chains: 8
• Total formula weight: 426807.14

Authors

Nair, S.K.,Agarwal, V. (deposition date: 2012-11-26, release date: 2013-11-27, Last modification date: 2024-02-28)

Primary citation

Agarwal, V.,Peck, S.C.,Chen, J.H.,Borisova, S.A.,Chekan, J.R.,van der Donk, W.A.,Nair, S.K.
Structure and function of phosphonoacetaldehyde dehydrogenase: the missing link in phosphonoacetate formation.
Chem.Biol., 21:125-135, 2014

PubMed Abstract: Phosphonates (C-PO₃²⁻) have applications as antibiotics, herbicides, and detergents. In some environments, these molecules represent the predominant source of phosphorus, and several microbes have evolved dedicated enzymatic machineries for phosphonate degradation. For example, most common naturally occurring phosphonates can be catabolized to either phosphonoacetaldehyde or phosphonoacetate, which can then be hydrolyzed to generate inorganic phosphate and acetaldehyde or acetate, respectively. The phosphonoacetaldehyde oxidase gene (phnY) links these two hydrolytic processes and provides a previously unknown catabolic mechanism for phosphonoacetate production in the microbial metabolome. Here, we present biochemical characterization of PhnY and high-resolution crystal structures of the apo state, as well as complexes with substrate, cofactor, and product. Kinetic analysis of active site mutants demonstrates how a highly conserved aldehyde dehydrogenase active site has been modified in nature to generate activity with a phosphonate substrate.

PubMed: 24361046
DOI: 10.1016/j.chembiol.2013.11.006

Experimental method

X-RAY DIFFRACTION (2.1 Å)