5ZPD | pdb_00005zpd

Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 288 K (1)

• PDB DOI: https://doi.org/10.2210/pdb5ZPD/pdb

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


• Deposited: 2018-04-16 Released: 2018-12-19 
• Deposition Author(s): Murakawa, T., Baba, S., Kawano, Y., Hayashi, H., Yano, T., Tanizawa, K., Kumasaka, T., Yamamoto, M., Okajima, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), JSPS KAKENHI

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

In crystallothermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase

Murakawa, T., Baba, S., Kawano, Y., Hayashi, H., Yano, T., Kumasaka, T., Yamamoto, M., Tanizawa, K., Okajima, T.

(2019) Proc Natl Acad Sci U S A 116: 135-140

• PubMed: 30563857 
• DOI: https://doi.org/10.1073/pnas.1811837116
• Primary Citation Related Structures: 
  5ZOU, 5ZOW, 5ZOX, 5ZOY, 5ZOZ, 5ZP0, 5ZP1, 5ZP2, 5ZP3, 5ZP4, 5ZP5, 5ZP6, 5ZP7, 5ZP8, 5ZP9, 5ZPA, 5ZPB, 5ZPC, 5ZPD, 5ZPE, 5ZPF, 5ZPG, 5ZPH, 5ZPI, 5ZPJ, 5ZPK, 5ZPL, 5ZPM, 5ZPN, 5ZPO, 5ZPP, 5ZPQ, 5ZPR, 5ZPS, 5ZPT


• PubMed Abstract: 
  

  In the catalytic reaction of copper amine oxidase, the protein-derived redox cofactor topaquinone (TPQ) is reduced by an amine substrate to an aminoresorcinol form (TPQ _amr ), which is in equilibrium with a semiquinone radical (TPQ _sq ). The transition from TPQ _amr to TPQ _sq is an endothermic process, accompanied by a significant conformational change of the cofactor. We employed the humid air and glue-coating (HAG) method to capture the equilibrium mixture of TPQ _amr and TPQ _sq in noncryocooled crystals of the enzyme from Arthrobacter globiformis and found that the equilibrium shifts more toward TPQ _sq in crystals than in solution. Thermodynamic analyses of the temperature-dependent equilibrium also revealed that the transition to TPQ _sq is entropy-driven both in crystals and in solution, giving the thermodynamic parameters that led to experimental determination of the crystal packing effect. Furthermore, we demonstrate that the binding of product aldehyde to the hydrophobic pocket in the active site produces various equilibrium states among two forms of the product Schiff-base, TPQ _amr , and TPQ _sq , in a pH-dependent manner. The temperature-controlled HAG method provides a technique for thermodynamic analysis of conformational changes occurring in protein crystals that are hardly scrutinized by conventional cryogenic X-ray crystallography.

---

Organizational Affiliation: 
• Department of Biochemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan.
Protein Crystal Analysis Division, Structure Analysis Promotion Group, Japan Synchrotron Radiation Research Institute, Sayo-gun, 679-5198 Hyogo, Japan.
Advanced Photon Technology Division, RIKEN SPring-8 Center, Sayo-gun, 679-5148 Hyogo, Japan.
Department of Chemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan.
Department of Biomolecular Science and Reaction, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047 Osaka, Japan.
Department of Chemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan; [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 138 kDa 
• Atom Count: 10,795 
• Modeled Residue Count: 1,240 
• Deposited Residue Count: 1,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylethylamine oxidase	A, B	620	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	C [auth A], E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYQ	A, B	L-PEPTIDE LINKING	C9 H12 N2 O4		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.603	α = 90
b = 64.612	β = 117.09
c = 158.869	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Murakawa, T., Baba, S., Kawano, Y., Hayashi, H., Yano, T., Tanizawa, K., Kumasaka, T., Yamamoto, M., Okajima, T.

---

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	0294
JSPS KAKENHI	Japan	17K07317, JP26440037, JP23770127, JP15K05573, JP16KT0055

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2019-01-02
  Changes: Data collection, Database references
• Version 1.2: 2019-01-16
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary