Calculating metalation in cells reveals CobW acquires CoII for vitamin B12 biosynthesis while related proteins prefer ZnII

• Published in: Nature communications Vol. 12; no. 1; p. 1195
• Main Authors: Young, Tessa R., Martini, Maria Alessandra, Foster, Andrew W., Glasfeld, Arthur, Osman, Deenah, Morton, Richard J., Deery, Evelyne, Warren, Martin J., Robinson, Nigel J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19-02-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 140/58; 38; 38/77; 639/638/45/612; 639/638/92/321; 639/638/92/96; 82/83; Affinity; Binding; Biosynthesis; Competition; Cyanocobalamin; Cytosol; Energy value; Free energy; Humanities and Social Sciences; Mathematical analysis; Metals; multidisciplinary; Nucleotides; Occupancy; Proteins; Science; Science (multidisciplinary); Sensors; Vitamin B12
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-21479-8

Protein metal-occupancy (metalation) in vivo has been elusive. To address this challenge, the available free energies of metals have recently been determined from the responses of metal sensors. Here, we use these free energy values to develop a metalation-calculator which accounts for inter-metal competition and changing metal-availabilities inside cells. We use the calculator to understand the function and mechanism of GTPase CobW, a predicted Co
II
-chaperone for vitamin B
12
. Upon binding nucleotide (GTP) and Mg
II
, CobW assembles a high-affinity site that can obtain Co
II
or Zn
II
from the intracellular milieu. In idealised cells with sensors at the mid-points of their responses, competition within the cytosol enables Co
II
to outcompete Zn
II
for binding CobW. Thus, Co
II
is the cognate metal. However, after growth in different [Co
II
], Co
II
-occupancy ranges from 10 to 97% which matches CobW-dependent B
12
synthesis. The calculator also reveals that related GTPases with comparable Zn
II
affinities to CobW, preferentially acquire Zn
II
due to their relatively weaker Co
II
affinities. The calculator is made available here for use with other proteins.
The connection between metal binding to proteins and availabilities of different metals in cells has been unclear. Here, the authors report a metalation-calculator that takes into account competition between metals and their variable accessibility, and thereby elucidate in vivo metal occupancies of three different proteins, CobW, YeiR and YjiA.