3S5W

Ornithine Hydroxylase (PvdA) from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Two Structures of an N-Hydroxylating Flavoprotein Monooxygenase: ORNITHINE HYDROXYLASE FROM PSEUDOMONAS AERUGINOSA.

Olucha, J.Meneely, K.M.Chilton, A.S.Lamb, A.L.

(2011) J Biol Chem 286: 31789-31798

  • DOI: 10.1074/jbc.M111.265876
  • Primary Citation of Related Structures:  
    3S61, 3S5W

  • PubMed Abstract: 
  • The ornithine hydroxylase from Pseudomonas aeruginosa (PvdA) catalyzes the FAD-dependent hydroxylation of the side chain amine of ornithine, which is subsequently formylated to generate the iron-chelating hydroxamates of the siderophore pyoverdin. PvdA b ...

    The ornithine hydroxylase from Pseudomonas aeruginosa (PvdA) catalyzes the FAD-dependent hydroxylation of the side chain amine of ornithine, which is subsequently formylated to generate the iron-chelating hydroxamates of the siderophore pyoverdin. PvdA belongs to the class B flavoprotein monooxygenases, which catalyze the oxidation of substrates using NADPH as the electron donor and molecular oxygen. Class B enzymes include the well studied flavin-containing monooxygenases and Baeyer-Villiger monooxygenases. The first two structures of a class B N-hydroxylating monooxygenase were determined with FAD in oxidized (1.9 Å resolution) and reduced (3.03 Å resolution) states. PvdA has the two expected Rossmann-like dinucleotide-binding domains for FAD and NADPH and also a substrate-binding domain, with the active site at the interface between the three domains. The structures have NADP(H) and (hydroxy)ornithine bound in a solvent-exposed active site, providing structural evidence for substrate and co-substrate specificity and the inability of PvdA to bind FAD tightly. Structural and biochemical evidence indicates that NADP(+) remains bound throughout the oxidative half-reaction, which is proposed to shelter the flavin intermediates from solvent and thereby prevent uncoupling of NADPH oxidation from hydroxylated product formation.


    Organizational Affiliation

    Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-ornithine 5-monooxygenase AB463Pseudomonas aeruginosaMutation(s): 0 
Gene Names: PA2386pvd-1pvdA
EC: 1.13.12 (PDB Primary Data), 1.14.13.195 (UniProt)
Find proteins for Q51548 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q51548 
Go to UniProtKB:  Q51548
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAP
Query on NAP

Download Ideal Coordinates CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
ONH
Query on ONH

Download Ideal Coordinates CCD File 
A, B
N~5~-hydroxy-L-ornithine
C5 H12 N2 O3
OZMJDTPATROLQC-BYPYZUCNSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.943α = 90
b = 130.943β = 90
c = 318.521γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-05-23 
  • Released Date: 2011-07-13 
  • Deposition Author(s): Olucha, J., Lamb, A.L.

Revision History 

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2011-07-27
    Changes: Database references
  • Version 1.2: 2011-09-21
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence