1IU7 | pdb_00001iu7

HOLO FORM OF COPPER-CONTAINING AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.252 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1IU7

This is version 1.3 of the entry. See complete history

Literature

Role of Copper Ion in Bacterial Copper Amine Oxidase: Spectroscopic and Crystallographic Studies of Metal-Substituted Enzymes

Kishishita, S.Okajima, T.Kim, M.Yamaguchi, H.Hirota, S.Suzuki, S.Kuroda, S.Tanizawa, K.Mure, M.

(2003) J Am Chem Soc 125: 1041-1055

  • DOI: https://doi.org/10.1021/ja017899k
  • Primary Citation Related Structures: 
    1IQX, 1IQY, 1IU7

  • PubMed Abstract: 

    The role of the active site Cu(2+) of phenylethylamine oxidase from Arthrobacter globiformis (AGAO) has been studied by substitution with other divalent cations, where we were able to remove >99.5% of Cu(2+) from the active site. The enzymes reconstituted with Co(2+) and Ni(2+) (Co- and Ni-AGAO) exhibited 2.2 and 0.9% activities, respectively, of the original Cu(2+)-enzyme (Cu-AGAO), but their K(m) values for amine substrate and dioxygen were comparable. X-ray crystal structures of the Co- and Ni-AGAO were solved at 2.0-1.8 A resolution. These structures revealed changes in the metal coordination environment when compared to that of Cu-AGAO. However, the hydrogen-bonding network around the active site involving metal-coordinating and noncoordinating water molecules was preserved. Upon anaerobic mixing of the Cu-, Co-, and Ni-AGAO with amine substrate, the 480 nm absorption band characteristic of the oxidized form of the topaquinone cofactor (TPQ(ox)) disappeared rapidly (< 6 ms), yielding the aminoresorcinol form of the reduced cofactor (TPQ(amr)). In contrast to the substrate-reduced Cu-AGAO, the semiquinone radical (TPQ(sq)) was not detected in Co- and Ni-AGAO. Further, in the latter, TPQ(amr) reacted reversibly with the product aldehyde to form a species with a lambda(max) at around 350 nm that was assigned as the neutral form of the product Schiff base (TPQ(pim)). Introduction of dioxygen to the substrate-reduced Co- and Ni-AGAO resulted in the formation of a TPQ-related intermediate absorbing at around 360 nm, which was assigned to the neutral iminoquinone form of the 2e(-)-oxidized cofactor (TPQ(imq)) and which decayed concomitantly with the generation of TPQ(ox). The rate of TPQ(imq) formation and its subsequent decay in Co- and Ni-AGAO was slow when compared to those of the corresponding reactions in Cu-AGAO. The low catalytic activities of the metal-substituted enzymes are due to the impaired efficiencies of the oxidative half-reaction in the catalytic cycle of amine oxidation. On the basis of these results, we propose that the native Cu(2+) ion has essential roles such as catalyzing the electron transfer between TPQ(amr) and dioxygen, in part by providing a binding site for 1e(-)- and 2e(-)-reduced dioxygen species to be efficiently protonated and released and also preventing the back reaction between the product aldehyde and TPQ(amr).


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

Macromolecule Content 

  • Total Structure Weight: 141.63 kDa 
  • Atom Count: 10,980 
  • Modeled Residue Count: 1,240 
  • Deposited Residue Count: 1,276 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AMINE OXIDASE
A, B
638Arthrobacter globiformisMutation(s): 1 
EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
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
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPQ
Query on TPQ
A, B
L-PEPTIDE LINKINGC9 H9 N O5TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.252 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.794α = 90
b = 62.633β = 111.74
c = 183.956γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-04
    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: 2023-12-27
    Changes: Data collection, Database references, Derived calculations