7DGM

The dimeric structure of K79H/G80A/H81A myoglobin

Summary for 7DGM

• Entry DOI: 10.2210/pdb7dgm/pdb
• Descriptor: Myoglobin, PROTOPORPHYRIN IX CONTAINING FE, OXYGEN ATOM, ... (4 entities in total)
• Functional Keywords: oxygen storage, oxygen binding
• Biological source: Equus caballus (Horse)
• Total number of polymer chains: 2
• Total formula weight: 35143.85

Authors

Nagao, S.,Idomoto, A.,Shibata, N.,Higuchi, Y.,Hirota, S. (deposition date: 2020-11-12, release date: 2021-02-17, Last modification date: 2023-11-29)

Primary citation

Nagao, S.,Idomoto, A.,Shibata, N.,Higuchi, Y.,Hirota, S.
Rational design of metal-binding sites in domain-swapped myoglobin dimers.
J.Inorg.Biochem., 217:111374-111374, 2021

PubMed Abstract: The metal active site is precisely designed in metalloproteins. Here we applied 3D domain swapping, a phenomenon in which a partial protein structure is exchanged between molecules, to introduce metal sites in proteins. We designed multiple metal-binding sites specific to domain-swapped myoglobin (Mb) with His mutation. Stable dimeric Mbs with metal-binding sites were obtained by shifting the His position and introducing two Ala residues in the hinge region (K78H/G80A/H82A and K79H/G80A/H81A Mbs). The absorption and circular dichroism spectra of the monomer and dimer of K78H/G80A/H82A and K79H/G80A/H81A Mbs were similar to the corresponding spectra, respectively, of wild-type Mb. No negative peak due to dimer-to-monomer dissociation was observed below the denaturation temperature in the differential scanning calorimetry thermograms of K78H/G80A/H82A and K79H/G80A/H81A Mbs, whereas the dimer dissociates into monomers at 68 °C for wild-type Mb. These results show that the two mutants were stable in the dimer state. Metal ions bound to the metal-binding sites containing the introduced His in the domain-swapped Mb dimers. Co-bound and Ni-bound K78H/G80A/H82A Mb exhibited octahedral metal-coordination structures, where His78, His81, Glu85, and three HO/OH molecules coordinated to the metal ion. On the other hand, Co-bound and Zn-bound K79H/G80A/H81A Mb exhibited tetrahedral metal-coordination structures, where His79, His82, Asp141, and a HO/OH molecule coordinated to the metal ion. The Co-bound site exists deep inside the protein in the K79H/G80A/H81A Mb dimer, which may allow the unique tetrahedral coordination for the Co ion. These results show that we can utilize domain swapping to construct artificial metalloproteins.

PubMed: 33578251
DOI: 10.1016/j.jinorgbio.2021.111374

Experimental method

X-RAY DIFFRACTION (1.62 Å)