Structural analysis of carboxyspermidine dehydrogenase from Helicobacter pylori
Kyung Yeol Ko1, Sun Cheol Park1, So Yeon Cho1
1Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Abstract:
Spermidine is a cationic polyamine that plays key roles in diverse biological processes, including biofilm formation and cell viability in bacteria. In some human gastrointestinal bacteria, such as Helicobacter pylori and Campylobacter jejuni, spermidine is biosynthesized using carboxyspermidine dehydrogenase (CASDH) and carboxyspermidine decarboxylase through an alternative pathway rather than the classical pathway found in most bacteria and eukaryotes. CASDH condenses putrescine and aspartate β-semialdehyde into carboxyspermidine in an NADPH-dependent manner. Because structural information on CASDH is not available, the exact enzymatic mechanism of CASDH has not been elucidated. To reveal the structural features of CASDH required for cofactor and substrate recruitment, we determined the crystal structures of the H. pylori CASDH protein alone and in complex with NADP. CASDH consists of three domains (D1, D2, and D3) and assembles into a homodimer exclusively using the D3 domain. The CASDH structure harbors a dent between the D1 and D3 domains. The NADP cofactor is inserted into the interdomain dent and induces structural rearrangements in CASDH, including dent closure and local structural changes in the D1 and D3 domains. A comparative analysis suggests that the substrate of CASDH binds in a cavity near the nicotinamide moiety of NADPH for the condensation reaction.
Insights
Carboxyspermidine dehydrogenase (CASDH) from Helicobacter pylori was structurally analyzed. NADP binding induces structural changes, revealing insights into spermidine biosynthesis mechanisms.
Area of Science:
- Biochemistry
- Structural Biology
- Microbiology
Background:
- Spermidine is a vital polyamine in bacterial processes like biofilm formation.
- Helicobacter pylori utilizes an alternative pathway for spermidine biosynthesis involving carboxyspermidine dehydrogenase (CASDH).
- The enzymatic mechanism of CASDH remains unclear due to a lack of structural data.
Purpose of the Study:
- To elucidate the structural basis of CASDH function.
- To understand cofactor and substrate recruitment mechanisms in CASDH.
- To provide insights into the alternative spermidine biosynthesis pathway.
Main Methods:
- Determined crystal structures of H. pylori CASDH alone and complexed with NADP.
- Analyzed the homodimeric structure of CASDH, highlighting domain interactions (D1, D2, D3).
- Investigated structural rearrangements upon NADP binding.
Main Results:
- CASDH forms a homodimer via the D3 domain, with a distinct dent between D1 and D3.
- NADP binding induces significant structural changes, including dent closure.
- A substrate-binding cavity near the NADPH nicotinamide moiety was identified.
Conclusions:
- The crystal structures reveal key features of CASDH for NADP and substrate binding.
- NADP-induced conformational changes are crucial for CASDH enzymatic activity.
- This study provides a structural foundation for understanding bacterial spermidine biosynthesis.
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