6L9C | pdb_00006l9c

Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4

• PDB DOI: https://doi.org/10.2210/pdb6L9C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arthrobacter globiformis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-11-08 Released: 2020-04-29 
• Deposition Author(s): Murakawa, T., Kurihara, K., Shoji, M., Shibazaki, C., Sunami, T., Tamada, T., Yano, N., Yamada, T., Kusaka, K., Suzuki, M., Shigeta, Y., Kuroki, R., Hayashi, H., Yano, Y., Tanizawa, K., Adachi, M., Okajima, T.
• Funding Organization(s): Japan Society for the Promotion of Science

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

---

• Method: NEUTRON DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.209 (Depositor) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.

Murakawa, T., Kurihara, K., Shoji, M., Shibazaki, C., Sunami, T., Tamada, T., Yano, N., Yamada, T., Kusaka, K., Suzuki, M., Shigeta, Y., Kuroki, R., Hayashi, H., Yano, T., Tanizawa, K., Adachi, M., Okajima, T.

(2020) Proc Natl Acad Sci U S A 117: 10818-10824

• PubMed: 32371483 
• DOI: https://doi.org/10.1073/pnas.1922538117
• Primary Citation Related Structures: 
  6L9C


• PubMed Abstract: 
  

  Recent advances in neutron crystallographic studies have provided structural bases for quantum behaviors of protons observed in enzymatic reactions. Thus, we resolved the neutron crystal structure of a bacterial copper (Cu) amine oxidase (CAO), which contains a prosthetic Cu ion and a protein-derived redox cofactor, topa quinone (TPQ). We solved hitherto unknown structures of the active site, including a keto/enolate equilibrium of the cofactor with a nonplanar quinone ring, unusual proton sharing between the cofactor and the catalytic base, and metal-induced deprotonation of a histidine residue that coordinates to the Cu. Our findings show a refined active-site structure that gives detailed information on the protonation state of dissociable groups, such as the quinone cofactor, which are critical for catalytic reactions.

---

Organizational Affiliation: 
• Department of Biochemistry, Osaka Medical College, 569-8686 Takatsuki, Osaka, Japan; [e-mail] [e-mail].
Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 319-1106 Tokai, Ibaraki, Japan.
Center for Computational Sciences, University of Tsukuba, 305-8577 Tsukuba, Ibaraki, Japan.
Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), 332-0012 Kawaguchi, Saitama, Japan.
Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 319-1106 Tokai, Ibaraki, Japan.
Institute for Protein Research, Osaka University, 565-0871 Suita, Osaka, Japan.
Quantum Beam Science Center, Japan Atomic Energy Agency, 319-1195 Tokai, Ibaraki, Japan.
Department of Chemistry, Osaka Medical College, 569-8686 Takatsuki, Osaka, Japan.
Department of Biochemistry, Osaka Medical College, 569-8686 Takatsuki, Osaka, Japan.
Institute of Scientific and Industrial Research, Osaka University, 567-0047 Ibaraki, Osaka, Japan.
Department of Chemistry, Osaka Medical College, 569-8686 Takatsuki, Osaka, Japan; [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 69.08 kDa 
• Atom Count: 6,258 
• Modeled Residue Count: 622 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylethylamine oxidase	A [auth X]	621	Arthrobacter globiformis	Mutation(s): 0  EC: 1.4.3.21
UniProt
Find proteins for P46881 (Arthrobacter globiformis) Explore P46881  Go to UniProtKB:  P46881

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	B [auth X]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NA	C [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ASA	A [auth X]	L-PEPTIDE LINKING	C4 H7 N O3		ASP
E9C	A [auth X]	L-PEPTIDE LINKING	C9 H9 N O5		TYR
TPQ	A [auth X]	L-PEPTIDE LINKING	C9 H9 N O5		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.209 (Depositor) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.548	α = 90
b = 61.779	β = 112.13
c = 92.332	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Murakawa, T., Kurihara, K., Shoji, M., Shibazaki, C., Sunami, T., Tamada, T., Yano, N., Yamada, T., Kusaka, K., Suzuki, M., Shigeta, Y., Kuroki, R., Hayashi, H., Yano, Y., Tanizawa, K., Adachi, M., Okajima, T.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP23770127, JP26440037, JP15K05573, JP16KT0055, 19K05694

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-05-20
  Changes: Database references
• Version 1.2: 2020-06-03
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description