3WA3

Crystal structure of copper amine oxidase from arthrobacter globiformis in N2 condition

Summary for 3WA3

• Entry DOI: 10.2210/pdb3wa3/pdb
• Related: 3WA2
• Descriptor: Phenylethylamine oxidase, COPPER (II) ION, SODIUM ION, ... (10 entities in total)
• Functional Keywords: oxidase, copper binding, post-translationally derived quinone cofactor, cytoplassm, oxidoreductase
• Biological source: Arthrobacter globiformis
• Total number of polymer chains: 2
• Total formula weight: 142793.93

Authors

Murakawa, T.,Hayashi, H.,Sunami, T.,Kurihara, K.,Tamada, T.,Kuroki, R.,Suzuki, M.,Tanizawa, K.,Okajima, T. (deposition date: 2013-04-22, release date: 2013-09-11, Last modification date: 2023-11-08)

Primary citation

Murakawa, T.,Hayashi, H.,Sunami, T.,Kurihara, K.,Tamada, T.,Kuroki, R.,Suzuki, M.,Tanizawa, K.,Okajima, T.
High-resolution crystal structure of copper amine oxidase from Arthrobacter globiformis: assignment of bound diatomic molecules as O2
Acta Crystallogr.,Sect.D, 69:2483-2494, 2013

PubMed Abstract: The crystal structure of a copper amine oxidase from Arthrobacter globiformis was determined at 1.08 Å resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight ∼200) as a cryoprotectant. The final crystallographic R factor and Rfree were 13.0 and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior, including the active site, which resulted in a marked reduction in the overall B factor and consequently led to a subatomic resolution structure for a relatively large protein with a monomer molecular weight of ∼70,000. About 40% of the presumed H atoms were observed as clear electron densities in the Fo - Fc difference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site, which contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely to be molecular oxygen, are bound to the protein, one of which is located in a region that had previously been proposed as an entry route for the dioxygen substrate from the central cavity of the dimer interface to the active site.

PubMed: 24311589
DOI: 10.1107/S0907444913023196

Experimental method

X-RAY DIFFRACTION (1.55 Å)