GO:0047125 delta1-piperideine-2-carboxylate reductase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0047125 describes the NADPH-dependent reduction of delta1-piperideine-2-carboxylate to L-pipecolate, the final step in lysine catabolism via the pipecolate pathway.
• The enzyme belongs to a distinct family of NAD(P)H-dependent oxidoreductases with a unique fold and conformational change upon substrate binding.
• It is found in bacteria such as Pseudomonas putida and in parasitic nematodes like Haemonchus contortus, where it supports lysine degradation [1,3].
• The reaction is reversible and uses NADP+ as the electron acceptor for the reverse oxidative direction.
• Studying this activity provides insights into lysine metabolism, nematode energy metabolism, and potential anthelmintic targets.
• CRISPR-based models (knockout, point mutation, knock-in, overexpression) enable precise functional dissection of this enzyme in diverse organisms.
Description
Delta1-piperideine-2-carboxylate reductase activity (GO:0047125) catalyzes the NADPH-dependent reduction of delta1-piperideine-2-carboxylate to L-pipecolate, a key step in the pipecolate pathway of lysine catabolism. This enzymatic activity was first characterized in Pseudomonas putida, where it facilitates the conversion of D-lysine to pipecolate [1,4]. The enzyme is also present in parasitic nematodes such as Haemonchus contortus and Teladorsagia circumcincta, where it contributes to lysine degradation and energy metabolism. Understanding this activity is important for researchers studying amino acid catabolism, microbial physiology, and host-parasite interactions. The crystal structure of the enzyme from Pseudomonas putida revealed a new family of NAD(P)H-dependent oxidoreductases, providing a structural basis for substrate recognition and catalysis. This article synthesizes authoritative QuickGO data and verified PubMed literature to provide a comprehensive overview of GO:0047125, its mechanism, associated genes, and research methodologies.
delta1-piperideine-2-carboxylate reductase activity At A Glance
| GO ID | GO:0047125 |
|---|---|
| GO term | delta1-piperideine-2-carboxylate reductase activity |
| Ontology | molecular_function |
| Synonym | 1,2-didehydropipecolate reductase activity; D1-piperideine-2-carboxylate reductase activity; L-pipecolate:NADP+ 2-oxidoreductase activity; P2C reductase activity |
| Definition | Catalysis of the reaction: NADP+ + L-pipecolate = NADPH + delta1-piperideine-2-carboxylate. |
| Major function | Reduction of delta1-piperideine-2-carboxylate to L-pipecolate in lysine catabolism |
| Cofactor | NADPH (reducing agent) / NADP+ (oxidizing agent) |
| Substrate | delta1-piperideine-2-carboxylate (forward reaction) or L-pipecolate (reverse reaction) |
| Product | L-pipecolate (forward reaction) or delta1-piperideine-2-carboxylate (reverse reaction) |
| EC number | 1.5.1.21 (not explicitly stated in QuickGO but implied by reaction) |
What Is GO:0047125?
GO:0047125 is defined as the catalysis of the reaction: NADP+ + L-pipecolate = NADPH + delta1-piperideine-2-carboxylate. In other words, it is an oxidoreductase activity that interconverts L-pipecolate and delta1-piperideine-2-carboxylate using NADP+/NADPH as a cofactor. This activity is synonymous with 1,2-didehydropipecolate reductase, D1-piperideine-2-carboxylate reductase, and L-pipecolate:NADP+ 2-oxidoreductase, among others.
Why Is delta1-piperideine-2-carboxylate reductase activity Important in Cell Biology?
GO:0047125 is important because it represents a critical enzymatic step in the pipecolate pathway of lysine catabolism, a route that allows organisms to utilize lysine as a carbon and energy source [1,3]. In bacteria like Pseudomonas putida, this activity is part of the D-lysine catabolic pathway encoded by the OCT plasmid. In parasitic nematodes, it supports lysine degradation, which may be essential for survival within the host. The enzyme's unique structural features make it a model for studying a new family of NAD(P)H-dependent oxidoreductases. Furthermore, because lysine metabolism is linked to various physiological processes, understanding this activity could inform research on metabolic disorders, microbial pathogenesis, and anthelmintic drug development.
• Catalyzes the final step in the pipecolate pathway of lysine catabolism.
• Enables Pseudomonas putida to grow on D-lysine as a sole carbon source.
• Supports lysine degradation in parasitic nematodes, potentially influencing host-parasite interactions.
• Represents a new family of NAD(P)H-dependent oxidoreductases with unique structural features.
• Provides a target for studying lysine metabolism disorders and metabolic engineering.
• Offers a potential drug target against parasitic nematodes.
• Facilitates comparative studies of amino acid catabolism across species.
• Enables mechanistic studies of reversible oxidoreduction and cofactor specificity [1,2].
What Happens During delta1-piperideine-2-carboxylate reductase activity?
Substrate Binding and Conformational Change
In simple terms: The enzyme changes shape to grab its substrate.
The enzyme binds delta1-piperideine-2-carboxylate in a specific pocket, triggering a conformational change that brings catalytic residues into position. This induced-fit mechanism ensures high substrate specificity and efficient catalysis.
Hydride Transfer from NADPH
In simple terms: NADPH donates a hydrogen to the substrate.
The reduced cofactor NADPH provides a hydride ion to the substrate's carbon-nitrogen double bond, reducing it to form L-pipecolate. The stereochemistry of the reaction is strictly controlled, yielding the L-isomer.
Product Release and Enzyme Reset
In simple terms: The product leaves, and the enzyme is ready for another round.
After reduction, L-pipecolate is released, and the enzyme returns to its original conformation, ready to bind another substrate molecule. The oxidized NADP+ is also released, allowing the cycle to continue.
Reverse Reaction and Cofactor Regeneration
In simple terms: The enzyme can also run backwards, using NADP+ to oxidize pipecolate.
The reaction is reversible; in the presence of NADP+, the enzyme oxidizes L-pipecolate back to delta1-piperideine-2-carboxylate. This reversibility allows the enzyme to participate in both catabolic and anabolic contexts depending on cellular needs.
Key Genes Involved in GO:0047125 delta1-piperideine-2-carboxylate reductase activity
The following genes and proteins are directly associated with delta1-piperideine-2-carboxylate reductase activity or its metabolic context.
| Gene | Major Role | Research Relevance |
|---|---|---|
| dpkA (Pseudomonas putida) | Encodes delta1-piperideine-2-carboxylate reductase | First characterized enzyme for GO:0047125; model for structural and mechanistic studies [1,2] |
| OCT plasmid genes | Encode D-lysine transport and catabolic enzymes | Provides genetic context for dpkA in D-lysine utilization |
| Haemonchus contortus homolog | Putative delta1-piperideine-2-carboxylate reductase | Potential role in lysine catabolism in parasitic nematodes |
| Teladorsagia circumcincta homolog | Putative delta1-piperideine-2-carboxylate reductase | Comparative studies of lysine degradation in nematodes |
| NADPH-dependent oxidoreductases (family) | Related enzymes with similar fold | Structural and evolutionary studies of the new family |
| L-lysine catabolic pathway genes | Upstream enzymes feeding into pipecolate pathway | Understanding metabolic flux and regulation [1,4] |
| Pipecolate oxidase (PIPOX) | Further metabolizes pipecolate in mammals | Potential link to human lysine metabolism disorders |
| Saccharopine dehydrogenase | Alternative lysine catabolic route | Comparative studies of lysine degradation pathways |
| D-lysine aminotransferase | Converts D-lysine to delta1-piperideine-2-carboxylate | Upstream enzyme in Pseudomonas putida |
| L-lysine 2-monooxygenase | Alternative route to pipecolate | Context for metabolic diversity |
| NADP+ transhydrogenase | Regenerates NADPH | Cofactor supply for reductase activity |
| Glutamate dehydrogenase | Links amino acid metabolism to TCA cycle | Metabolic integration |
| Pipecolate dehydrogenase | Oxidizes pipecolate | Reverse pathway component |
| Lysine decarboxylase | Produces cadaverine from lysine | Competing pathway |
| Ornithine cyclodeaminase | Produces proline from ornithine | Related amino acid metabolism |
| Proline dehydrogenase | Degrades proline | Similar flavin-dependent oxidoreductase |
| Delta1-pyrroline-2-carboxylate reductase | Reduces a similar substrate | Structural and functional homolog |
| D-lysine transporter | Uptake of D-lysine | Essential for catabolism in Pseudomonas |
How Is delta1-piperideine-2-carboxylate reductase activity Regulated?
The regulation of delta1-piperideine-2-carboxylate reductase activity is not well characterized in the provided literature. In Pseudomonas putida, the OCT plasmid encodes the entire D-lysine catabolic pathway, suggesting that expression may be induced by the presence of D-lysine. However, specific transcriptional regulators or post-translational modifications have not been described in the verified citations. Further research is needed to elucidate regulatory mechanisms.
delta1-piperideine-2-carboxylate reductase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| dpkA (Pseudomonas putida) | D-lysine catabolism, opportunistic infections | Knockout in P. putida to assess growth on D-lysine |
| Haemonchus contortus homolog | Parasitic infection in livestock | RNAi knockdown or CRISPR knockout in nematode models |
| Teladorsagia circumcincta homolog | Parasitic infection in livestock | CRISPR knockout in nematode models |
| Human PIPOX | Hyperlysinemia, pipecolic acidemia | Knockout in human cell lines to study lysine metabolism |
| NADPH-dependent oxidoreductases | Metabolic disorders, cancer metabolism | Overexpression or knockout in cancer cell lines |
Parasitic Nematode Infections
Haemonchus contortus and Teladorsagia circumcincta are parasitic nematodes that cause significant disease in livestock. Their ability to catabolize lysine via delta1-piperideine-2-carboxylate reductase may be crucial for survival within the host, making this enzyme a potential target for anthelmintic drugs.
Lysine Metabolism Disorders
In humans, defects in lysine catabolism can lead to hyperlysinemia and related metabolic disorders. While the pipecolate pathway is not the primary route in humans, understanding enzymes like delta1-piperideine-2-carboxylate reductase can provide insights into alternative metabolic routes and their potential roles in disease.
Bacterial Pathogenesis
Pseudomonas putida is an opportunistic pathogen, and its ability to utilize D-lysine via the OCT plasmid-encoded pathway may contribute to its survival in diverse environments. The reductase activity is part of this catabolic arsenal.
From delta1-piperideine-2-carboxylate reductase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| What is the role of dpkA in D-lysine utilization? | Knockout of dpkA in Pseudomonas putida |
| How does the enzyme's structure affect catalysis? | Point mutations in catalytic residues of dpkA |
| Can the enzyme be targeted for anthelmintic therapy? | Knockout or knockdown in Haemonchus contortus |
| What is the metabolic flux through the pipecolate pathway? | Knock-in of tagged enzyme for flux analysis |
| Does overexpression affect lysine catabolism? | Overexpression of dpkA in P. putida or E. coli |
| How is the enzyme regulated? | Promoter-reporter knock-in in P. putida |
How to Study the delta1-piperideine-2-carboxylate reductase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Spectrophotometric assay | NADPH oxidation/reduction | Enzyme kinetics and inhibitor testing |
| X-ray crystallography | Three-dimensional structure | Active site and conformational analysis |
| CRISPR knockout | Gene function | Phenotypic analysis in P. putida or nematodes |
| RNA-seq | Gene expression | Transcriptional response to D-lysine |
| Proteomics | Protein abundance | Enzyme levels under different conditions |
| Site-directed mutagenesis | Residue function | Catalytic mechanism |
| Enzyme-linked immunosorbent assay | Protein quantification | Expression analysis |
| Metabolic flux analysis | Pathway activity | Lysine catabolism flux |
Enzymatic Assays
Direct measurement of delta1-piperideine-2-carboxylate reductase activity can be performed spectrophotometrically by monitoring NADPH oxidation at 340 nm. This method is suitable for kinetic studies and inhibitor screening.
X-ray Crystallography
Crystal structures of the enzyme in complex with substrate analogs or cofactors reveal the molecular basis of catalysis and conformational changes. This method provides high-resolution insights into the active site.
CRISPR-Cas9 Knockout
Generating knockout cell lines or organisms lacking the gene encoding this activity allows researchers to assess its physiological role in lysine catabolism and growth.
RNA-seq and Proteomics
Transcriptomic and proteomic profiling can reveal expression patterns of the enzyme under different conditions, such as D-lysine induction in Pseudomonas putida.
How CRISPR Can Be Used to Study GO:0047125 delta1-piperideine-2-carboxylate reductase activity
Knockout
CRISPR-Cas9 knockout of the gene encoding delta1-piperideine-2-carboxylate reductase (e.g., dpkA in Pseudomonas putida) can abolish the enzyme's activity, allowing researchers to study its role in D-lysine catabolism and growth. In parasitic nematodes, knockout can reveal essentiality for survival.
Point Mutation
Introducing point mutations in catalytic residues (e.g., those identified in the crystal structure) can dissect the mechanism of hydride transfer and substrate specificity. This approach helps validate structural models and identify key residues.
Knock-in
Knock-in of tagged versions of the enzyme (e.g., GFP or FLAG) enables localization, purification, and interaction studies. This can be achieved via CRISPR-mediated homology-directed repair in model organisms.
Overexpression
CRISPR activation (CRISPRa) or plasmid-based overexpression can increase enzyme levels, facilitating biochemical characterization and metabolic engineering for lysine catabolism.
How EDITGENE Supports delta1-piperideine-2-carboxylate reductase activity Research
Researchers studying delta1-piperideine-2-carboxylate reductase activity-related genes often need to determine whether a candidate gene is causally involved in lysine catabolism, metabolic disorders, or parasite survival. EDITGENE provides a comprehensive suite of CRISPR services to enable precise genetic modifications in various model systems.
Contact EDITGENE today to design your custom CRISPR model for delta1-piperideine-2-carboxylate reductase activity research.
Frequently Asked Questions About delta1-piperideine-2-carboxylate reductase activity
What is delta1-piperideine-2-carboxylate reductase activity?
It is an enzymatic activity (GO:0047125) that catalyzes the NADPH-dependent reduction of delta1-piperideine-2-carboxylate to L-pipecolate, a step in lysine catabolism.
What genes are involved in delta1-piperideine-2-carboxylate reductase activity?
The dpkA gene in Pseudomonas putida encodes this enzyme, and homologs exist in parasitic nematodes like Haemonchus contortus [1,3].
What is the reaction catalyzed by GO:0047125?
NADP+ + L-pipecolate = NADPH + delta1-piperideine-2-carboxylate, as defined by QuickGO.
Which organisms have delta1-piperideine-2-carboxylate reductase?
It is found in bacteria such as Pseudomonas putida and in parasitic nematodes like Haemonchus contortus and Teladorsagia circumcincta [1,3].
What is the role of delta1-piperideine-2-carboxylate reductase in lysine catabolism?
It catalyzes the final step in the pipecolate pathway, converting delta1-piperideine-2-carboxylate to L-pipecolate.
How can I study delta1-piperideine-2-carboxylate reductase activity?
You can use enzymatic assays, X-ray crystallography, CRISPR knockout, and RNA-seq, among other methods [1,2,4].
Is delta1-piperideine-2-carboxylate reductase a potential drug target?
In parasitic nematodes, it may be a target for anthelmintic drugs, but further research is needed.
What is the structure of delta1-piperideine-2-carboxylate reductase?
Crystal structures have revealed a new family of NAD(P)H-dependent oxidoreductases with a unique fold and conformational change upon substrate binding.
What cofactor does delta1-piperideine-2-carboxylate reductase use?
It uses NADPH as the reducing agent and NADP+ as the oxidizing agent.
Can CRISPR be used to study delta1-piperideine-2-carboxylate reductase?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression are powerful tools to dissect its function.
Conclusion
Delta1-piperideine-2-carboxylate reductase activity (GO:0047125) is a key enzymatic step in the pipecolate pathway of lysine catabolism, with representatives in bacteria and parasitic nematodes. Its unique structural features and metabolic role make it an attractive subject for mechanistic and applied research. By leveraging CRISPR-based models and other advanced methodologies, researchers can uncover its physiological functions and potential as a therapeutic target. EDITGENE's comprehensive services support these endeavors, from knockout to overexpression and screening.
References
- 1. Payton CW et al.. 1982. delta1-piperideine-2-carboxylate reductase of Pseudomonas putida.. J Bacteriol 149(3):864-71 PMID: 6801013
- 2. Goto M et al.. 2005. Crystal structures of Delta1-piperideine-2-carboxylate/Delta1-pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction.. J Biol Chem 280(49):40875-84 PMID: 16192274
- 3. Umair S et al.. 2012. Lysine catabolism in Haemonchus contortus and Teladorsagia circumcincta.. Exp Parasitol 131(1):101-6 PMID: 22459625
- 4. Cao X et al.. 1993. The OCT plasmid encodes D-lysine membrane transport and catabolic enzymes in Pseudomonas putida.. Plasmid 30(2):83-9 PMID: 8234494
