Structure and Function of Proline Catabolic Enzymes

Proline catabolism is a central metabolic pathway that converts the amino acid proline into glutamate, thereby linking amino acid turnover, redox balance and energy production. In bacteria and eukaryotes, this conversion occurs via two successive oxidations: the FAD-dependent proline dehydrogenase (PRODH) reaction, which yields Δ¹-pyrroline-5-carboxylate (P5C), and the NAD⁺-dependent P5C dehydrogenase (P5CDH) reaction, which produces glutamate. In many bacteria, a single multifunctional flavoenzyme known as Proline Utilization A (PutA) harbours both PRODH and P5CDH activities, often complemented by regulatory domains that control gene expression in response to proline availability. The three-dimensional architectures of these enzymes reveal a conserved core fold for the PRODH and P5CDH modules, while accessory domains facilitate substrate channeling, oligomer assembly and membrane association. Substrate channeling ensures efficient transfer of the reactive intermediate P5C between active sites, minimising its escape into the cytosol. Allosteric conformational changes and quaternary rearrangements underpin regulation, as illustrated by class-specific domain interfaces and ligand-induced dimerization. In mammals, monofunctional PRODH plays roles in oxidative stress, apoptosis and tumour suppression, with therapeutic implications arising from its propensity to generate reactive oxygen species under certain conditions. Collectively, structural and kinetic studies have illuminated how active-site geometry, cofactor selection and interdomain communication govern catalytic efficiency and regulatory versatility in proline catabolic enzymes.

Research from Nature Portfolio

Recent structural work on Thermus thermophilus PRODH has challenged the paradigm of FAD specificity in flavoenzymes. Crystallographic and biochemical analyses revealed that the TIM-barrel fold of this PRODH binds FAD and FMN with comparable affinity and activity, prompting a reassessment of cofactor classification in proline oxidases. In parallel, functional annotation of an uncharacterised aconitase family member has identified a novel cis-3-hydroxy-L-proline dehydratase activity. Electron paramagnetic resonance and mutational mapping of its mononuclear Fe centre established a distinct mechanism within the aconitase superfamily and expanded understanding of hydroxyproline metabolism in bacteria.

Structure and Function of Proline Catabolic Enzymes publication trend

The graph below shows the total number of articles in structure and function of proline catabolic enzymes across all publications each year (not limited to Nature Index journals).

Technical terms

PRODH: Proline dehydrogenase, a FAD-dependent enzyme catalysing the oxidation of proline to Δ¹-pyrroline-5-carboxylate.

P5CDH: Pyrroline-5-carboxylate dehydrogenase, an NAD⁺-dependent enzyme converting P5C to glutamate.

PutA: A bifunctional flavoenzyme combining PRODH and P5CDH activities, often with regulatory domains for gene control.

Substrate channeling: A mechanism by which intermediates are directly transferred between enzyme active sites without complete diffusion into the bulk solvent.

Flavoenzyme: An enzyme that utilises a flavin cofactor (FAD or FMN) to facilitate redox reactions.

References

1. Identification and Characterization of the DNA-binding Domain of the Multifunctional PutA Flavoenzyme*. Journal of Biological Chemistry (2004).
2. Structures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function*. Journal of Biological Chemistry (2016).
3. Structure and characterization of a class 3B proline utilization A: Ligand-induced dimerization and importance of the C-terminal domain for catalysis. Journal of Biological Chemistry (2017).
4. Proline dehydrogenase from Thermus thermophilus does not discriminate between FAD and FMN as cofactor. Scientific Reports (2017).
5. Functional characterization of aconitase X as a cis-3-hydroxy-L-proline dehydratase. Scientific Reports (2016).
6. Computational insights on the hydride and proton transfer mechanisms of L-proline dehydrogenase. PLOS ONE (2023).
7. N-Propargylglycine: a unique suicide inhibitor of proline dehydrogenase with anticancer activity and brain-enhancing mitohormesis properties. Amino Acids (2021).