ESRF Highlights 2021

S T R U C T U R A L B I O L O G Y

S C I E N T I F I C H I G H L I G H T S

5 4 H I G H L I G H T S 2 0 2 1 I

PRINCIPAL PUBLICATION AND AUTHORS

The SOUL family of heme-binding proteins: Structure and function 15 years later, B.J. Goodfellow (a), F. Freire (b,c), A.L. Carvalho (d), S.S. Aveiro (e), P. Charbonnier (f), J.-M. Moulis (f,g), L. Delgado (h), G.C. Ferreira (i), J.E. Rodrigues (j), P. Poussin- Courmontagne (k), C. Birck (k), A. McEwen (k), A.L. Macedo (d), Coord. Chem. Rev. 448, 214189 (2021); https:/doi.org/10.1016/j.ccr.2021.214189 (a) CICECO, Departamento de Química, Universidade de Aveiro (Portugal) (b) iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras (Portugal) (c) Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras (Portugal) (d) UCIBIO - Applied Molecular Biosciences Unit, Departamento de Química, and Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School

of Science and Technology, Universidade NOVA de Lisboa, Caparica (Portugal) (e) GreenCoLab - Associação Oceano Verde, Universidade do Algarve, Campus de Gambelas, Faro (Portugal) (f) University Grenoble-Alpes, CEA Grenoble, Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Grenoble (France) (g) University Grenoble-Alpes, Laboratory of Fundamental and Applied Bioenergetics (LBFA), Inserm U1055, Grenoble (France) (h) Equity Analyst Biotech & Healthcare, Baader Helvea, Zurich (Switzerland) (i) Department of Molecular Medicine, Morsani College of Medicine, University of South Florida (USA) (j) CNC, Universidade de Coimbra, Faculdade de Medicina, Coimbra (Portugal) (k) Integrated Structural Biology Platform, CBI-IGBMC, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch (France)

REFERENCES

[1] J.S. Dias et al., J. Biol. Chem. 281, 31553-31561 (2006). [2] E. Ambrosi et al., Biochem. J. 438, 291-301 (2011). [3] S. Taketani et al., J. Biol. Chem. 273, 31388-31394 (1998).

ring to be obtained, which confirmed that only hydrophobic interactions play a role in tetrapyrrole binding [3].

Figure 41a shows the hydrophobic binding site in mHEBP1 with the residues within 4 Å of the bound heme ring displayed in blue. The heme is oriented with the propionate acid groups directed toward the solvent. A putative mobile loop, located above the bound heme, is shown in purple. In Figure 41b, three methionine residues that may be important for binding and that are close to the bound heme (not shown) are indicated. Human HEBP2 with only 28% sequence identity with mHEBP1 presents a very similar 3D fold to the HEBP1 structures. However, no interaction with tetrapyrroles has been detected. By superimposing the

Fig. 41: The mHEBP1-heme X-ray crystal structure

(7OON, chain A) shown with (a) the heme ligand in red and residues with atoms within 4 Å

of the ligand highlighted in light blue. An unstructured loop is

shown in purple. b) The same orientation as in (a) but with the heme ligand hidden and

the residues labelled. The hydrophobic binding pocket

contains 3 methionines (59, 63 and 78), V80 and V82.

The orientation of the heme ring directs the propionate side

chains towards the solvent.

heme-bound mHEBP1 structure on hHEBP2 and removing the HEBP1 chain, it is evident, in Figure 42, that hHEBP2 has a bulky Phenylalanine group (F66) that would inhibit heme binding in that same location even if a similar hydrophobic pocket existed.

In summary, although HEBP1 and HEBP2 are currently placed in the same protein family, it is now clear why HEBP1 binds heme strongly while HEBP2 does not. It may no longer be justified to call this very small family of proteins heme-binding proteins . The family may be more correctly called the SOUL family of proteins related to cellular fate , as both proteins may be involved in cell survival and/or proliferation.

Fig. 42: The hHEBP2 X-ray structure (4B0Y) and the heme ring (red) from the mHEBP1

X-ray structure (7OON) superimposed after backbone alignment (rmsd 1.16 Å). Residues for hHEBP2 within 4 Å of the heme group in

the superimposed structures are shown in blue. The proximity of the F66 and N70 side chains to the heme ring would impede binding in an

equivalent position in hHEBP2.