9EAF

Carboxyspermidine decarboxylase from Clostridium leptum

Summary for 9EAF

• Entry DOI: 10.2210/pdb9eaf/pdb
• Descriptor: Carboxynorspermidine decarboxylase, HIS-HIS-HIS-SER-SER-GLY-LEU-VAL, POTASSIUM ION, ... (6 entities in total)
• Functional Keywords: spermidine, decarboxylase, pyridoxal 5-phosphate, polyamine biosynthesis, bacterial, biosynthetic protein
• Biological source: [Clostridium] leptum; More
• Total number of polymer chains: 4
• Total formula weight: 85578.02

Authors

Jones, S.J.,Bell, D.J.,McFarlane, J.S. (deposition date: 2024-11-10, release date: 2025-02-12, Last modification date: 2025-03-05)

Primary citation

Jones, S.J.,Bell, D.J.,McFarlane, J.S.
Structure of Clostridium leptum carboxyspermidine decarboxylase and comparison to homologs prevalent within the human gut microbiome.
Acta Crystallogr.,Sect.F, 81:66-72, 2025

PubMed Abstract: Polyamines are key signalling and substrate molecules that are made by all organisms. The polyamine known as spermidine is typically made by spermidine synthase, but in many bacterial species, including 70% of human gut microbes, carboxyspermidine decarboxylase (CASDC) performs the terminal step in the production of spermidine. An X-ray crystal structure of CASDC from the human gut microbe Clostridium leptum has been solved by molecular replacement at a resolution of 1.41 Å. CASDC is a homodimer, with each monomer composed of two domains: a β/α-barrel pyridoxal 5'-phosphate-binding domain that forms most of the active site and a β-barrel domain that extends the dimeric interface and contributes to the active site of the opposing monomer. We performed a structural comparison of CASDC enzymes for 15 common genera within the human gut flora. This analysis reveals structural differences occurring in the β6/β7 loop that acts as a `flap' covering the active site and in the α9/β12 loop that is connected to the α9 helix which is thought to select substrates by their chain length. This structural analysis extends our understanding of a key enzyme in spermidine biosynthesis in many bacterial species.

PubMed: 39887002
DOI: 10.1107/S2053230X25000482

Experimental method

X-RAY DIFFRACTION (1.41 Å)