9PPN
Cu-bound structure of the H77C variant of TriCyt2
Summary for 9PPN
| Entry DOI | 10.2210/pdb9ppn/pdb |
| Descriptor | Soluble cytochrome b562, COPPER (II) ION (3 entities in total) |
| Functional Keywords | cu-binding protein, assembly, metal binding protein |
| Biological source | Escherichia coli BL21(DE3) |
| Total number of polymer chains | 3 |
| Total formula weight | 35701.97 |
| Authors | |
| Primary citation | Eng, V.H.,Gascon, M.,Kakkis, A.,Tezcan, F.A. Design of a protein scaffold with a selective, Bi-containing heterodinuclear metal coordination motif. J.Inorg.Biochem., 274:113104-113104, 2025 Cited by PubMed Abstract: The design of proteins with selective metal-binding properties to accommodate distinct metal ions remains a challenge in the field of artificial metalloprotein design. Here, we report our design approach to incorporate heterodinuclear metal coordination motifs along the interface of a trimeric protein assembly, termed TriCyt2, that enables the selective binding of the post-transition metal ion Bi(III) and a first-row transition metal ion (M(II)). The coordination sites are composed of soft tris-Cys donors and intermediate/hard tris-His centers that are placed proximally to one another within the highly stable, preorganized trimeric architecture of TriCyt2 to allow for the formation of a heterodinuclear center. We obtained crystal structures (at 2.5 Å resolution or better) of the TriCyt2 trimer complexed with a first-row transition metal (Mn(II), Co(II), Ni(II), Cu(II), or Zn(II)) that binds at the tris-His site, and a TriCyt2 structure complexed with Bi(III) at the tris-Cys site, thereby confirming the selectivity of metal binding motifs as designed. Additionally, we obtained the crystal structures of BiCo, BiNi, and BiZn heterodinuclear proteins, and demonstrated through solution experiments that the trimeric state of TriCyt2 is maintained upon the concomitant addition of Bi(III) and various M(II) species. Structural analyses of the mononuclear and heterodinuclear TriCyt2 structures further revealed different Bi(III) binding geometries in each case, which indicated that the preferential coordination geometries of the transition metal ions can influence the Bi(III) coordination geometry and that subtle structural changes within the protein structure may promote or disfavor Bi(III) binding. PubMed: 41072111DOI: 10.1016/j.jinorgbio.2025.113104 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.87 Å) |
Structure validation
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