1IVV

Crystal structure of copper amine oxidase from Arthrobacter globiformis: Early intermediate in topaquinone biogenesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

X-ray snapshots of quinone cofactor biogenesis in bacterial copper amine oxidase.

Kim, M.Okajima, T.Kishishita, S.Yoshimura, M.Kawamori, A.Tanizawa, K.Yamaguchi, H.

(2002) Nat Struct Biol 9: 591-596

  • DOI: https://doi.org/10.1038/nsb824
  • Primary Citation of Related Structures:  
    1IVU, 1IVV, 1IVW, 1IVX

  • PubMed Abstract: 

    The quinone cofactor TPQ in copper amine oxidase is generated by posttranslational modification of an active site tyrosine residue. Using X-ray crystallography, we have probed the copper-dependent autooxidation process of TPQ in the enzyme from Arthrobacter globiformis. Apo enzyme crystals were anaerobically soaked with copper; the structure determined from this crystal provides a view of the initial state: the unmodified tyrosine coordinated to the bound copper. Exposure of the copper-bound crystals to oxygen led to the formation of freeze-trapped intermediates; structural analyses indicate that these intermediates contain dihydroxyphenylalanine quinone and trihydroxyphenylalanine. These are the first visualized intermediates during TPQ biogenesis in copper amine oxidase.


  • Organizational Affiliation

    School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
amine oxidase
A, B
638Arthrobacter globiformisMutation(s): 0 
EC: 1.4.3.6
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DAH
Query on DAH
A, B
L-PEPTIDE LINKINGC9 H11 N O4PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.802α = 90
b = 63.069β = 111.64
c = 183.461γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-08-31
    Changes: Non-polymer description
  • Version 1.4: 2019-10-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations