Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin

Takahide Yamaguchi; Attila Taborosi; Chihiro Sakai; Kohei Akao; Seiji Mori; Takamitsu Kohzuma

doi:10.1016/j.jinorgbio.2023.112292

Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin

J Inorg Biochem. 2023 Sep:246:112292. doi: 10.1016/j.jinorgbio.2023.112292. Epub 2023 Jun 15.

Authors

Takahide Yamaguchi¹, Attila Taborosi², Chihiro Sakai³, Kohei Akao³, Seiji Mori¹, Takamitsu Kohzuma⁴

Affiliations

¹ Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan.
² Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Research Initiative for Supra-Materials, Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano, Nagano 380-8553, Japan.
³ Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan.
⁴ Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan. Electronic address: takamitsu.kohzuma.qbs@vc.ibaraki.ac.jp.

PMID: 37354604
DOI: 10.1016/j.jinorgbio.2023.112292

Abstract

The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.

Keywords: Blue copper protein; Noncovalent interactions; Second coordination sphere.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Azurin* / chemistry
Azurin* / metabolism
Catalytic Domain
Copper* / chemistry
Crystallography, X-Ray
Models, Molecular

Substances

pseudoazurin
Copper
Azurin