1H84

COVALENT ADDUCT BETWEEN POLYAMINE OXIDASE AND N1ethylN11((cycloheptyl)methyl)4,8diazaundecane at pH 4.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Bases for Inhibitor Binding and Catalysis in Polyamine Oxidase

Binda, C.Angelini, R.Federico, R.Ascenzi, P.Mattevi, A.

(2001) Biochemistry 40: 2766

  • Primary Citation of Related Structures:  1H81, 1H82, 1H83, 1H86

  • PubMed Abstract: 
  • Polyamine oxidase (PAO) carries out the FAD-dependent oxidation of the secondary amino groups of spermidine and spermine, a key reaction in the polyamine catabolism. The active site of PAO consists of a 30 A long U-shaped catalytic tunnel, whose inne ...

    Polyamine oxidase (PAO) carries out the FAD-dependent oxidation of the secondary amino groups of spermidine and spermine, a key reaction in the polyamine catabolism. The active site of PAO consists of a 30 A long U-shaped catalytic tunnel, whose innermost part is located in front of the flavin ring. To provide insight into the PAO substrate specificity and amine oxidation mechanism, we have investigated the crystal structure of maize PAO in the reduced state and in complex with three different inhibitors, guazatine, 1,8-diaminooctane, and N(1)-ethyl-N(11)-[(cycloheptyl)methyl]-4,8-diazaundecane (CHENSpm). In the reduced state, the conformation of the isoalloxazine ring and the surrounding residues is identical to that of the oxidized enzyme. Only Lys300 moves away from the flavin to compensate for the change in cofactor protonation occurring upon reduction. The structure of the PAO.inhibitor complexes reveals an exact match between the inhibitors and the PAO catalytic tunnel. Inhibitor binding does not involve any protein conformational change. Such lock-and-key binding occurs also in the complex with CHENSpm, which forms a covalent adduct with the flavin N5 atom. Comparison of the enzyme complexes hints at an "out-of-register" mechanism of inhibition, in which the inhibitor secondary amino groups are not properly aligned with respect to the flavin to allow oxidation. Except for the Glu62-Glu170 pair, no negatively charged residues are involved in the recognition of substrate and inhibitor amino groups, which is in contrast to other polyamine binding proteins. This feature may be exploited in the design of drugs specifically targeting PAO.


    Organizational Affiliation

    Dipartimento di Genetica e Microbiologia, Università di Pavia, Via Abbiategrasso 207, I-27100 Pavia, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POLYAMINE OXIDASE
A, B, C
472Zea maysGene Names: PAO
EC: 1.5.3.14, 1.5.3.15
Find proteins for O64411 (Zea mays)
Go to UniProtKB:  O64411
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FCA
Query on FCA

Download SDF File 
Download CCD File 
C
ALPHA-D-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-PHYPRBDBSA-N
 Ligand Interaction
NBA
Query on NBA

Download SDF File 
Download CCD File 
A, B, C
3-[(3-{[3-(METHYLAMINO)PROPYL]AMINO}PROPYL)AMINO]PROPANE-1,1-DIOL
C10 H25 N3 O2
PTLIEDFKZYQZEI-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 184.040α = 90.00
b = 184.040β = 90.00
c = 280.800γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4phasing
SCALAdata scaling
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-31
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Data collection, Derived calculations, Non-polymer description, Other, Version format compliance