7N4F

Ni-bound crystal structure of the engineered cyt cb562 variant, AB2-H100A, crystallized in the presence of Ni(II)

Summary for 7N4F

• Entry DOI: 10.2210/pdb7n4f/pdb
• Descriptor: Soluble cytochrome b562, HEME C, NICKEL (II) ION, ... (4 entities in total)
• Functional Keywords: metal selectivity, irving-williams series, metal binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 24992.31

Authors

Choi, T.S.,Tezcan, F.A. (deposition date: 2021-06-04, release date: 2022-06-15, Last modification date: 2024-10-23)

Primary citation

Choi, T.S.,Tezcan, F.A.
Overcoming universal restrictions on metal selectivity by protein design.
Nature, 603:522-527, 2022

PubMed Abstract: Selective metal coordination is central to the functions of metalloproteins: each metalloprotein must pair with its cognate metallocofactor to fulfil its biological role. However, achieving metal selectivity solely through a three-dimensional protein structure is a great challenge, because there is a limited set of metal-coordinating amino acid functionalities and proteins are inherently flexible, which impedes steric selection of metals. Metal-binding affinities of natural proteins are primarily dictated by the electronic properties of metal ions and follow the Irving-Williams series (Mn < Fe < Co < Ni < Cu > Zn) with few exceptions. Accordingly, metalloproteins overwhelmingly bind Cu and Zn in isolation, regardless of the nature of their active sites and their cognate metal ions. This led organisms to evolve complex homeostatic machinery and non-equilibrium strategies to achieve correct metal speciation. Here we report an artificial dimeric protein, (AB), that thermodynamically overcomes the Irving-Williams restrictions in vitro and in cells, favouring the binding of lower-Irving-Williams transition metals over Cu, the most dominant ion in the Irving-Williams series. Counter to the convention in molecular design of achieving specificity through structural preorganization, (AB) was deliberately designed to be flexible. This flexibility enabled (AB) to adopt mutually exclusive, metal-dependent conformational states, which led to the discovery of structurally coupled coordination sites that disfavour Cu ions by enforcing an unfavourable coordination geometry. Aside from highlighting flexibility as a valuable element in protein design, our results illustrate design principles for constructing selective metal sequestration agents.

PubMed: 35236987
DOI: 10.1038/s41586-022-04469-8

Experimental method

X-RAY DIFFRACTION (1.8 Å)