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AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the Heavy-Metal Associated superfamily
  • +5
  • Isabelle Callebaut,
  • Geoffroy Gaschignard,
  • Maxime Millet,
  • Apolline Bruley,
  • Karim Benzerara,
  • Manuela Dezi,
  • Feriel Skouri-Panet,
  • Elodie Duprat
Isabelle Callebaut
Sorbonne Universite UFR de Physique

Corresponding Author:[email protected]

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Geoffroy Gaschignard
Sorbonne Universite UFR de Physique
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Maxime Millet
Sorbonne Universite UFR de Physique
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Apolline Bruley
Sorbonne Universite UFR de Physique
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Karim Benzerara
Sorbonne Universite UFR de Physique
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Manuela Dezi
Sorbonne Universite UFR de Physique
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Feriel Skouri-Panet
Sorbonne Universite UFR de Physique
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Elodie Duprat
Sorbonne Universite UFR de Physique
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Abstract

Three-dimensional structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches and (iii) the use of AlphaFold2 3D structure models. Domains of this family called CoBaHMA, were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most CoBaHMA domains share conserved basic amino acids, forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
26 Sep 2023Submitted to PROTEINS: Structure, Function, and Bioinformatics
29 Sep 2023Submission Checks Completed
29 Sep 2023Assigned to Editor
29 Sep 2023Review(s) Completed, Editorial Evaluation Pending
30 Sep 2023Reviewer(s) Assigned
22 Nov 2023Editorial Decision: Revise Major