7JRQ

Crystallographically Characterized De Novo Designed Mn-Diphenylporphyrin Binding Protein

Summary for 7JRQ

• Entry DOI: 10.2210/pdb7jrq/pdb
• Descriptor: MPP1, GLYCEROL, [5,15-diphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]manganese, ... (5 entities in total)
• Functional Keywords: metalloprotein, porphyrin, oxidation, sulfoxidation, high-talent, helical bundle, de novo protein
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 16653.68

Authors

Mann, S.I.,DeGrado, W.F. (deposition date: 2020-08-12, release date: 2021-01-13, Last modification date: 2023-10-18)

Primary citation

Mann, S.I.,Nayak, A.,Gassner, G.T.,Therien, M.J.,DeGrado, W.F.
De Novo Design, Solution Characterization, and Crystallographic Structure of an Abiological Mn-Porphyrin-Binding Protein Capable of Stabilizing a Mn(V) Species.
J.Am.Chem.Soc., 143:252-259, 2021

PubMed Abstract: protein design offers the opportunity to test our understanding of how metalloproteins perform difficult transformations. Attaining high-resolution structural information is critical to understanding how such designs function. There have been many successes in the design of porphyrin-binding proteins; however, crystallographic characterization has been elusive, limiting what can be learned from such studies as well as the extension to new functions. Moreover, formation of highly oxidizing high-valent intermediates poses design challenges that have not been previously implemented: (1) purposeful design of substrate/oxidant access to the binding site and (2) limiting deleterious oxidation of the protein scaffold. Here we report the first crystallographically characterized porphyrin-binding protein that was programmed to not only bind a synthetic Mn-porphyrin but also maintain binding site access to form high-valent oxidation states. We explicitly designed a binding site with accessibility to dioxygen units in the open coordination site of the Mn center. In solution, the protein is capable of accessing a high-valent Mn(V)-oxo species which can transfer an O atom to a thioether substrate. The crystallographic structure is within 0.6 Å of the design and indeed contained an aquo ligand with a second water molecule stabilized by hydrogen bonding to a Gln side chain in the active site, offering a structural explanation for the observed reactivity.

PubMed: 33373215
DOI: 10.1021/jacs.0c10136

Experimental method

X-RAY DIFFRACTION (1.75 Å)