5ZPE

Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 288 K (2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.689 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1073/pnas.1811837116
  • Primary Citation of Related Structures:  

  • 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 <sub>amr </sub>), which is in equilibrium with a semiquinone radical (TPQ <sub>sq ...

    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

    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; tokajima@sanken.osaka-u.ac.jp.,Department of Biochemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan.,Department of Chemistry, 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.,Department of Biomolecular Science and Reaction, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047 Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylethylamine oxidase
A, B
620Arthrobacter globiformisMutation(s): 0 
EC: 1.4.3.21
Find proteins for P46881 (Arthrobacter globiformis)
Go to UniProtKB:  P46881
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYQ
Query on TYQ
A, B
L-PEPTIDE LINKINGC9 H12 N2 O4TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.689 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.151 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 193.558α = 90.00
b = 64.465β = 117.12
c = 158.831γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan0294
JSPS KAKENHIJapan17K07317, JP26440037, JP23770127, JP15K05573, JP16KT0055

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-02
    Type: Data collection, Database references
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references