3NBB

Crystal structure of mutant Y305F expressed in E. coli in the copper amine oxidase from hansenula polymorpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity.

Chen, Z.W.Datta, S.Dubois, J.L.Klinman, J.P.Mathews, F.S.

(2010) Biochemistry 49: 7393-7402

  • DOI: 10.1021/bi100643y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site ...

    The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.


    Related Citations: 
    • Copper amine oxidase from Hansenula polymorpha: the crystal structure determined at 2.4 A resolution reveals the active conformation.
      Li, R.,Klinman, J.P.,Mathews, F.S.
      (1998) Structure 6: 293


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, Box 8231, St. Louis, Missouri 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisomal primary amine oxidase
A, B, C, D, E, F
692Pichia angustaMutation(s): 1 
Gene Names: AMO
EC: 1.4.3.21
Find proteins for P12807 (Pichia angusta)
Go to UniProtKB:  P12807
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D, E, F
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
TY9
Query on TY9
A, B, C, D, E, F
L-peptide linkingC9 H11 N O7TYR
TY8
Query on TY8
A, B, C, D, E, F
L-peptide linkingC9 H11 N O7TYR
ME0
Query on ME0
A, B, C, D, E, F
L-peptide linkingC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.523α = 90.00
b = 232.618β = 91.51
c = 104.146γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance