6L9C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1073/pnas.1922538117
  • Primary Citation of 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) ...

    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

    Institute of Scientific and Industrial Research, Osaka University, 567-0047 Ibaraki, Osaka, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylethylamine oxidaseA [auth X]621Arthrobacter globiformisMutation(s): 0 
EC: 1.4.3.21
UniProt
Find proteins for P46881 (Arthrobacter globiformis)
Explore P46881 
Go to UniProtKB:  P46881
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46881
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
B [auth X]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth X]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ASA
Query on ASA
A [auth X]L-PEPTIDE LINKINGC4 H7 N O3ASP
E9C
Query on E9C
A [auth X]L-PEPTIDE LINKINGC9 H9 N O5TYR
TPQ
Query on TPQ
A [auth X]L-PEPTIDE LINKINGC9 H9 N O5TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.548α = 90
b = 61.779β = 112.13
c = 92.332γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP23770127, JP26440037, JP15K05573, JP16KT0055, 19K05694

Revision History  (Full details and data files)

  • 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