1PBY

Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution.

Datta, S.Ikeda, T.Kano, K.Mathews, F.S.

(2003) Acta Crystallogr.,Sect.D 59: 1551-1556


  • PubMed Abstract: 
  • The 109 kDa quinohemoprotein amine dehydrogenase (QHNDH) from Paracoccus denitrificans contains a novel redox cofactor, cysteine tryptophylquinone (CTQ). This cofactor is derived from a pair of gene-encoded amino acids by post-translational modificat ...

    The 109 kDa quinohemoprotein amine dehydrogenase (QHNDH) from Paracoccus denitrificans contains a novel redox cofactor, cysteine tryptophylquinone (CTQ). This cofactor is derived from a pair of gene-encoded amino acids by post-translational modification and was previously identified and characterized within an 82-residue subunit by chemical methods and crystallographic analysis at 2.05 A resolution. It contains an orthoquinone moiety bound to the indole ring and catalyzes the oxidation of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms. This paper reports the structural analysis of the complex of QHNDH with the enzyme inhibitor phenylhydrazine determined at 1.70 A resolution. The phenylhydrazone product is attached to the C6 position, identifying the O6 atom of CTQ as the site of Schiff-base formation as postulated by analogy to another amine-oxidizing enzyme, methylamine dehydrogenase. Furthermore, the inner N atom closest to the phenyl ring of phenylhydrazine forms a hydrogen bond to gammaAsp33 in the complex, lending support to the hypothesis that this residue serves as the active-site base for proton abstraction during catalysis.


    Organizational Affiliation

    Washington University School of Medicine, St Louis, MO 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
quinohemoprotein amine dehydrogenase 60 kDa subunit
A
489Paracoccus denitrificansN/A
Find proteins for Q8VUT0 (Paracoccus denitrificans)
Go to UniProtKB:  Q8VUT0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
quinohemoprotein amine dehydrogenase 40 kDa subunit
B
337Paracoccus denitrificansN/A
Find proteins for Q8VUS7 (Paracoccus denitrificans)
Go to UniProtKB:  Q8VUS7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
quinohemoprotein amine dehydrogenase 9 kDa subunit
C
79Paracoccus denitrificansGene Names: qhnDH
EC: 1.4.99.-
Find proteins for Q8VUS8 (Paracoccus denitrificans)
Go to UniProtKB:  Q8VUS8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
TBU
Query on TBU

Download SDF File 
Download CCD File 
A, B
TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TRW
Query on TRW
C
L-PEPTIDE LINKINGC17 H18 N4 O2TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 99.237α = 90.00
b = 99.237β = 90.00
c = 213.056γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description