7D9F

SpdH Spermidine dehydrogenase SeMet Structure

Summary for 7D9F

• Entry DOI: 10.2210/pdb7d9f/pdb
• Descriptor: Spermidine dehydrogenase, SpdH, FLAVIN-ADENINE DINUCLEOTIDE, PROTOPORPHYRIN IX CONTAINING FE, ... (6 entities in total)
• Functional Keywords: spdh, spermidine dehydrogenase, heme-containing monoamine oxidase, pseudomonas aeruginosa pao1., oxidoreductase
• Biological source: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
• Total number of polymer chains: 2
• Total formula weight: 142764.95

Authors

Che, S.,Zhang, Q.,Bartlam, M. (deposition date: 2020-10-13, release date: 2021-11-17, Last modification date: 2024-10-30)

Primary citation

Che, S.,Liang, Y.,Chen, Y.,Wu, W.,Liu, R.,Zhang, Q.,Bartlam, M.
Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold.
Febs J., 289:1911-1928, 2022

PubMed Abstract: The opportunistic pathogen Pseudomonas aeruginosa can utilize polyamines (including putrescine, cadaverine, 4-aminobutyrate, spermidine, and spermine) as its sole source of carbon and nitrogen. Spermidine dehydrogenase (SpdH) is a component of one of the two polyamine utilization pathways identified in P. aeruginosa, but little is known about its structure and function. Here, we report the first crystal structure of SpdH from P. aeruginosa to 1.85 Å resolution. The resulting core structure confirms that SpdH belongs to the polyamine oxidase (PAO) family with flavin-binding and substrate-binding domains. A unique N-terminal extension wraps around the flavin-binding domain of SpdH and is required for heme binding, placing a heme cofactor in close proximity to the FAD cofactor. Structural and mutational analysis reveals that residues in the putative active site at the re side of the FAD isoalloxazine ring form part of the catalytic machinery. PaSpdH features an unusual active site and lacks the conserved lysine that forms part of a lysine-water-flavin N5 atom interaction in other PAO enzymes characterized to date. Mutational analysis further confirms that heme is required for catalytic activity. This work provides an important starting point for understanding the role of SpdH, which occurs universally in P. aeruginosa strains, in polyamine metabolism.

PubMed: 34741591
DOI: 10.1111/febs.16264

Experimental method

X-RAY DIFFRACTION (1.85 Å)