7YRK | pdb_00007yrk

Crystal structure of the hen egg lysozyme-2-oxidobenzylidene-threoninato-copper (II) complex

• PDB DOI: https://doi.org/10.2210/pdb7YRK/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2022-08-10 Released: 2023-05-10 
• Deposition Author(s): Unno, M., Furuya, T., Kitanishi, K., Akitsu, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 
  0.128 (Depositor), 0.127 (DCC) 
• R-Value Work: 
  0.113 (Depositor), 0.113 (DCC) 
• R-Value Observed: 
  0.114 (Depositor) 

Starting Model: experimental

Literature

A novel hybrid protein composed of superoxide-dismutase-active Cu(II) complex and lysozyme.

Furuya, T., Nakane, D., Kitanishi, K., Katsuumi, N., Tsaturyan, A., Shcherbakov, I.N., Unno, M., Akitsu, T.

(2023) Sci Rep 13: 6892-6892

• PubMed: 37106030 
• DOI: https://doi.org/10.1038/s41598-023-33926-1
• Primary Citation Related Structures: 
  7YRK


• PubMed Abstract: 
  

  A novel hybrid protein composed of a superoxide dismutase-active Cu(II) complex (CuST) and lysozyme (CuST@lysozyme) was prepared. The results of the spectroscopic and electrochemical analyses confirmed that CuST binds to lysozyme. We determined the crystal structure of CuST@lysozyme at 0.92 Å resolution, which revealed that the His15 imidazole group of lysozyme binds to the Cu(II) center of CuST in the equatorial position. In addition, CuST was fixed in position by the weak axial coordination of the Thr89 hydroxyl group and the hydrogen bond between the guanidinium group of the Arg14 residue and the hydroxyl group of CuST. Furthermore, the combination of CuST with lysozyme did not decrease the superoxide dismutase activity of CuST. Based on the spectral, electrochemical, structural studies, and quantum chemical calculations, an O ₂ ^- disproportionation mechanism catalyzed by CuST@lysozyme is proposed.

---

Organizational Affiliation: 
• Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan.
Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan. [e-mail].
Université Jean Monnet Saint-Etienne, CNRS, Institut d Optique Graduate School, Laboratoire Hubert Curien UMR 5516, 42023, Saint-Étienne, France.
Institute of Physical and Organic Chemistry, Southern Federal University, 194/2 Stachka Ave., Rostov-On-Don, 344090, Russia.
Department of Chemistry, Southern Federal University, 7 Zorge Str., Rostov-On-Don, 344090, Russia.
Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki, 316-8511, Japan.
Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.89 kDa 
• Atom Count: 1,400 
• Modeled Residue Count: 129 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	147	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JI6 (Subject of Investigation/LOI)	D [auth A]	(6~{S})-6-[(1~{R})-1-oxidanylethyl]-2,4-dioxa-7$l^{4}-aza-3$l^{3}-cupratricyclo[7.4.0.0^{3,7}]trideca-1(13),7,9,11-tetraen-5-one C11 H11 Cu N O4 RLMUPHKMYNMLMB-NBDMYRNNSA-L
EDO	B [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	I [auth A], J [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN	A	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free:  0.128 (Depositor), 0.127 (DCC) 
• R-Value Work:  0.113 (Depositor), 0.113 (DCC) 
• R-Value Observed: 0.114 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.671	α = 90
b = 78.671	β = 90
c = 37.203	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Unno, M., Furuya, T., Kitanishi, K., Akitsu, T.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H00336

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 2.0: 2024-09-25
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary