1D6Z

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

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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • DOI: 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 ...

    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.

    Related Citations: 
    • The Active Site Base Controls Cofactor Reactivity in Escherichia coli Amine Oxidase: X-ray Crystallographic Studies with Mutational Variants.
      Murray, J.M., Saysell, C.G., Wilmot, C.M., Tambyrajah, W.S., Jaeger, J., Knowles, P.F., Phillips, S.E., McPherson, M.J.
      (1999) Biochemistry 38: 8217
    • Catalytic Mechanism of the Quinoenzyme Amine Oxidase from Escherichia coli: Exploring the Reductive Half-Reaction.
      Wilmot, C.M., Murray, J.M., Alton, G., Parsons, M.R., Convery, M.A., Blakeley, V., Corner, A.S., Palcic, M.M., Knowles, P.F., McPherson, M.J., Knowles, P.F.
      (1997) Biochemistry 36: 1608
    • Crystal Structure of a Quinoenzyme: Copper Amine Oxidase of Escherichia coli at 2 Angstroms Resolution.
      Parsons, M.R., Convery, M.A., Wilmot, C.M., Yadav, K.D.S., Blakeley, V., Corner, A.S., Phillips, S.E., McPherson, M.J., Knowles, P.F.
      (1995) Structure 3: 1171
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COPPER AMINE OXIDASEA, B727Escherichia coliMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46883
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEA
Query on PEA
Download Ideal Coordinates CCD File 
H [auth A]2-PHENYLETHYLAMINE
C8 H12 N
BHHGXPLMPWCGHP-UHFFFAOYSA-O		 Ligand Interaction
HY1
Query on HY1
Download Ideal Coordinates CCD File 
F [auth A],
M [auth B]		PHENYLACETALDEHYDE
C8 H8 O
DTUQWGWMVIHBKE-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
I [auth A],
O [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CU
Query on CU
Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
K [auth B],
L [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
PEO
Query on PEO
Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]		HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYY
Query on TYY		A, B L-PEPTIDE LINKINGC9 H10 N2 O4TYR
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 = 135.236α = 90
b = 166.482β = 90
c = 79.628γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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