5I93

Structure of Mouse Acireductone dioxygenase with Ni2+ and 2-ketopentanoic acid in the active site

Summary for 5I93

• Entry DOI: 10.2210/pdb5i93/pdb
• Related: 5I8S 5I8Y 5I91
• Descriptor: 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase, NICKEL (II) ION, 2-oxopentanoic acid, ... (4 entities in total)
• Functional Keywords: 2-oxovaleric acid, oxidoreductase
• Biological source: Mus musculus (Mouse)
• Total number of polymer chains: 1
• Total formula weight: 21729.38

Authors

Deshpande, A.R.,Wagenpfeil, K.,Pochapsky, T.C.,Petsko, G.A.,Ringe, D. (deposition date: 2016-02-19, release date: 2016-03-09, Last modification date: 2023-09-27)

Primary citation

Deshpande, A.R.,Wagenpfeil, K.,Pochapsky, T.C.,Petsko, G.A.,Ringe, D.
Metal-Dependent Function of a Mammalian Acireductone Dioxygenase.
Biochemistry, 55:1398-1407, 2016

PubMed Abstract: The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella oxytoca are the only known pair of naturally occurring metalloenzymes with distinct chemical and physical properties determined solely by the identity of the divalent transition metal ion (Fe(2+) or Ni(2+)) in the active site. We now show that this dual chemistry can also occur in mammals. ARD from Mus musculus (MmARD) was studied to relate the metal ion identity and three-dimensional structure to enzyme function. The iron-containing isozyme catalyzes the cleavage of 1,2-dihydroxy-3-keto-5-(thiomethyl)pent-1-ene (acireductone) by O2 to formate and the ketoacid precursor of methionine, which is the penultimate step in methionine salvage. The nickel-bound form of ARD catalyzes an off-pathway reaction resulting in formate, carbon monoxide (CO), and 3-(thiomethyl) propionate. Recombinant MmARD was expressed and purified to obtain a homogeneous enzyme with a single transition metal ion bound. The Fe(2+)-bound protein, which shows about 10-fold higher activity than that of others, catalyzes on-pathway chemistry, whereas the Ni(2+), Co(2+), or Mn(2+) forms exhibit off-pathway chemistry, as has been seen with ARD from Klebsiella. Thermal stability of the isozymes is strongly affected by the metal ion identity, with Ni(2+)-bound MmARD being the most stable, followed by Co(2+) and Fe(2+), and Mn(2+)-bound ARD being the least stable. Ni(2+)- and Co(2+)-bound MmARD were crystallized, and the structures of the two proteins found to be similar. Enzyme-ligand complexes provide insight into substrate binding, metal coordination, and the catalytic mechanism.

PubMed: 26858196
DOI: 10.1021/acs.biochem.5b01319

Experimental method

X-RAY DIFFRACTION (2.236 Å)