Structure of Agmatinase from Klebsiella pneumoniae and the Active Site Comparison with Its Structural Homologues

Agmatinase (SpeB) catalyzes the hydrolysis of agmatine to produce putrescine, a key step in bacterial polyamine biosynthesis. Here, we report the crystal structure of SpeB from Klebsiella pneumoniae (kpSpeB) and characterize its oligomeric and active-site architecture. SEC–MALS analysis demonstrates that kpSpeB forms a canonical hexamer in solution. Structural comparison reveals high similarity to Escherichia coli SpeB and other members of the arginase superfamily, including proclavaminic acid amidino hydrolase (PAH) and guanidine hydrolase (GdmH). Despite strong conservation of residues coordinating the binuclear Mn²⁺ center, subtle differences in metal positioning and cavity geometry were observed. Surface analysis indicates variations in active-site cavity volume among homologues, with partial occlusion in GdmH due to a bulky tryptophan residue. These findings suggest that minor adjustments in metal coordination and cavity architecture may fine-tune substrate selectivity while preserving the conserved catalytic framework of the arginase superfamily.