6UIY

Artificial Iron Proteins: Modelling the Active Sites in Non-Heme Dioxygenases

Summary for 6UIY

• Entry DOI: 10.2210/pdb6uiy/pdb
• Descriptor: Streptavidin, {5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-{[(pyridin-2-yl)methyl][(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)pentanamide}iron(2+), ACETATE ION, ... (4 entities in total)
• Functional Keywords: biotin binding artificial metalloprotein, metal binding protein
• Biological source: Streptomyces avidinii
• Total number of polymer chains: 1
• Total formula weight: 17195.51

Authors

Miller, K.R.,Paretsky, J.D.,Follmer, A.H.,Heinisch, T.,Mittra, K.,Gul, S.,Kim, I.-S.,Fuller, F.D.,Batyuk, A.,Sutherlin, K.D.,Brewster, A.S.,Bhowmick, A.,Sauter, N.K.,Kern, J.,Yano, J.,Green, M.T.,Ward, T.R.,Borovik, A.S. (deposition date: 2019-10-01, release date: 2020-05-06, Last modification date: 2023-10-11)

Primary citation

Miller, K.R.,Paretsky, J.D.,Follmer, A.H.,Heinisch, T.,Mittra, K.,Gul, S.,Kim, I.S.,Fuller, F.D.,Batyuk, A.,Sutherlin, K.D.,Brewster, A.S.,Bhowmick, A.,Sauter, N.K.,Kern, J.,Yano, J.,Green, M.T.,Ward, T.R.,Borovik, A.S.
Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases.
Inorg.Chem., 59:6000-6009, 2020

PubMed Abstract: An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the SE mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic Fe complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from SE. Two aqua ligands complete the primary coordination sphere of the Fe center with both involved in hydrogen bond networks within Sav. The corresponding Fe protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The Fe protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.

PubMed: 32309932
DOI: 10.1021/acs.inorgchem.9b03791

Experimental method

X-RAY DIFFRACTION (1.47 Å)