6EZZ

Crystal structure of Escherichia coli amine oxidase mutant E573Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Oxygen Activation Switch in the Copper Amine Oxidase of Escherichia coli.

Gaule, T.G.Smith, M.A.Tych, K.M.Pirrat, P.Trinh, C.H.Pearson, A.R.Knowles, P.F.McPherson, M.J.

(2018) Biochemistry 57: 5301-5314

  • DOI: 10.1021/acs.biochem.8b00633
  • Primary Citation of Related Structures:  
    6EZZ, 6GRR

  • PubMed Abstract: 
  • Copper amine oxidases (CuAOs) are metalloenzymes that reduce molecular oxygen to hydrogen peroxide during catalytic turnover of primary amines. In addition to Cu 2+ in the active site, two peripheral calcium sites, ∼32 Å from the active site, have roles in Escherichia coli amine oxidase (ECAO) ...

    Copper amine oxidases (CuAOs) are metalloenzymes that reduce molecular oxygen to hydrogen peroxide during catalytic turnover of primary amines. In addition to Cu 2+ in the active site, two peripheral calcium sites, ∼32 Å from the active site, have roles in Escherichia coli amine oxidase (ECAO). The buried Ca 2+ (Asp533, Leu534, Asp535, Asp678, and Ala679) is essential for full-length protein production, while the surface Ca 2+ (Glu573, Tyr667, Asp670, and Glu672) modulates biogenesis of the 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor. The E573Q mutation at the surface site prevents calcium binding and TPQ biogenesis. However, TPQ biogenesis can be restored by a suppressor mutation (I342F) in the proposed oxygen delivery channel to the active site. While supporting TPQ biogenesis (∼60% WTECAO TPQ), I342F/E573Q has almost no amine oxidase activity (∼4.6% WTECAO activity). To understand how these long-range mutations have major effects on TPQ biogenesis and catalysis, we employed ultraviolet-visible spectroscopy, steady-state kinetics, inhibition assays, and X-ray crystallography. We show that the surface metal site controls the equilibrium (disproportionation) of the Cu 2+ -substrate reduced TPQ (TPQ AMQ ) Cu + -TPQ semiquinone (TPQ SQ ) couple. Removal of the calcium ion from this site by chelation or mutagenesis shifts the equilibrium to Cu 2+ -TPQ AMQ or destabilizes Cu + -TPQ SQ . Crystal structure analysis shows that TPQ biogenesis is stalled at deprotonation in the Cu 2+ -tyrosinate state. Our findings support WTECAO using the inner sphere electron transfer mechanism for oxygen reduction during catalysis, and while a Cu + -tyrosyl radical intermediate is not essential for TPQ biogenesis, it is required for efficient biogenesis.


    Organizational Affiliation

    Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Primary amine oxidaseA, B727Escherichia coli K-12Mutation(s): 1 
Gene Names: tynAmaoAb1386JW1381
EC: 1.4.3.21
UniProt
Find proteins for P46883 (Escherichia coli (strain K12))
Explore P46883 
Go to UniProtKB:  P46883
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , N [auth B] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  N [auth B],  O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
C [auth A], L [auth B]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A], M [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.521α = 90
b = 167.202β = 90
c = 79.939γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/C00468X/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references