3NBJ

Crystal Structure of Y305F mutant of the copper amine oxidase from Hansenula polymorpha expressed in yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1021/bi100643y
  • Primary Citation of Related Structures:  
    3N9H, 3NBB, 3NBJ

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisomal primary amine oxidase
A, B, C, D, E
A, B, C, D, E, F
692Ogataea angustaMutation(s): 1 
Gene Names: AMO
EC: 1.4.3.21
UniProt
Find proteins for P12807 (Pichia angusta)
Explore P12807 
Go to UniProtKB:  P12807
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12807
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth F]
DA [auth F]
H [auth A]
I [auth A]
BA [auth F],
CA [auth F],
DA [auth F],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth C],
T [auth D],
U [auth D],
V [auth D],
X [auth E],
Y [auth E],
Z [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CU
Query on CU

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
K [auth B]
O [auth C]
S [auth D]
AA [auth F],
G [auth A],
K [auth B],
O [auth C],
S [auth D],
W [auth E]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
ME0
Query on ME0
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O3 SMET
TY8
Query on TY8
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC9 H11 N O7TYR
TY9
Query on TY9
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC9 H11 N O7TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.29α = 90
b = 232.47β = 93.68
c = 104.31γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-22
    Changes: Data collection