1D6Z

CRYSTAL STRUCTURE OF THE AEROBICALLY FREEZE TRAPPED RATE-DETERMINING CATALYTIC INTERMEDIATE OF E. COLI COPPER-CONTAINING AMINE OXIDASE.

• PDB DOI: https://doi.org/10.2210/pdb1D6Z/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-10-16 Released: 2000-02-02 
• Deposition Author(s): Wilmot, C.M., Hajdu, J., McPherson, M.J., Knowles, P.F., Phillips, S.E.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.237 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Visualization of dioxygen bound to copper during enzyme catalysis.

Wilmot, C.M., Hajdu, J., McPherson, M.J., Knowles, P.F., Phillips, S.E.

(1999) Science 286: 1724-1728

• PubMed: 10576737 
• DOI: https://doi.org/10.1126/science.286.5445.1724
• Primary Citation of Related Structures:  
  1D6U, 1D6Y, 1D6Z


• PubMed Abstract: 
  

  X-ray crystal structures of three species related to the oxidative half of the reaction of the copper-containing quinoprotein amine oxidase from Escherichia coli have been determined. Crystals were freeze-trapped either anaerobically or aerobically after exposure to substrate, and structures were determined to resolutions between 2.1 and 2.4 angstroms. The oxidation state of the quinone cofactor was investigated by single-crystal spectrophotometry. The structures reveal the site of bound dioxygen and the proton transfer pathways involved in oxygen reduction. The quinone cofactor is regenerated from the iminoquinone intermediate by hydrolysis involving Asp383, the catalytic base in the reductive half-reaction. Product aldehyde inhibits the hydrolysis, making release of product the rate-determining step of the reaction in the crystal.

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Organizational Affiliation: 

Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

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)

Macromolecule Content

• Total Structure Weight: 163.63 kDa 
• Atom Count: 12,842 
• Modelled Residue Count: 1,438 
• Deposited Residue Count: 1,454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COPPER AMINE OXIDASE	A, B	727	Escherichia coli	Mutation(s): 1  EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt
Find proteins for P46883 (Escherichia coli (strain K12)) Explore P46883  Go to UniProtKB:  P46883

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEA	H [auth A]	2-PHENYLETHYLAMINE C8 H12 N BHHGXPLMPWCGHP-UHFFFAOYSA-O
HY1	F [auth A], M [auth B]	PHENYLACETALDEHYDE C8 H8 O DTUQWGWMVIHBKE-UHFFFAOYSA-N
GOL	I [auth A], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	C [auth A], J [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	D [auth A], E [auth A], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
PEO	G [auth A], N [auth B]	HYDROGEN PEROXIDE H2 O2 MHAJPDPJQMAIIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYY	A, B	L-PEPTIDE LINKING	C9 H10 N2 O4		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.237 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.236	α = 90
b = 166.482	β = 90
c = 79.628	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-02 
Deposition Author(s): Wilmot, C.M., Hajdu, J., McPherson, M.J., Knowles, P.F., Phillips, S.E.V.

Revision History  

• Version 1.0: 2000-02-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.5: 2024-11-13
  Changes: Structure summary