5UPB

Swit_4259, an Acetoacetate Decarboxylase-like Enzyme from Sphingomonas wittichii RW1

Summary for 5UPB

• Entry DOI: 10.2210/pdb5upb/pdb
• Descriptor: Acetoacetate decarboxylase (2 entities in total)
• Functional Keywords: acetoacetate decarboxylase-like enzyme, lyase
• Biological source: Sphingomonas wittichii
• Total number of polymer chains: 4
• Total formula weight: 110897.44

Authors

Mydy, L.S.,Silvaggi, N.R. (deposition date: 2017-02-02, release date: 2017-06-07, Last modification date: 2023-10-04)

Primary citation

Mydy, L.S.,Mashhadi, Z.,Knight, T.W.,Fenske, T.,Hagemann, T.,Hoppe, R.W.,Han, L.,Miller, T.R.,Schwabacher, A.W.,Silvaggi, N.R.
Swit_4259, an acetoacetate decarboxylase-like enzyme from Sphingomonas wittichii RW1.
Acta Crystallogr F Struct Biol Commun, 73:672-681, 2017

PubMed Abstract: The Gram-negative bacterium Sphingomonas wittichii RW1 is notable for its ability to metabolize a variety of aromatic hydrocarbons. Not surprisingly, the S. wittichii genome contains a number of putative aromatic hydrocarbon-degrading gene clusters. One of these includes an enzyme of unknown function, Swit_4259, which belongs to the acetoacetate decarboxylase-like superfamily (ADCSF). Here, it is reported that Swit_4259 is a small (28.8 kDa) tetrameric ADCSF enzyme that, unlike the prototypical members of the superfamily, does not have acetoacetate decarboxylase activity. Structural characterization shows that the tertiary structure of Swit_4259 is nearly identical to that of the true decarboxylases, but there are important differences in the fine structure of the Swit_4259 active site that lead to a divergence in function. In addition, it is shown that while it is a poor substrate, Swit_4259 can catalyze the hydration of 2-oxo-hex-3-enedioate to yield 2-oxo-4-hydroxyhexanedioate. It is also demonstrated that Swit_4259 has pyruvate aldolase-dehydratase activity, a feature that is common to all of the family V ADCSF enzymes studied to date. The enzymatic activity, together with the genomic context, suggests that Swit_4259 may be a hydratase with a role in the metabolism of an as-yet-unknown hydrocarbon. These data have implications for engineering bioremediation pathways to degrade specific pollutants, as well as structure-function relationships within the ADCSF in general.

PubMed: 29199988
DOI: 10.1107/S2053230X17015862

Experimental method

X-RAY DIFFRACTION (1.912 Å)