Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100106.70 
• Atom Count: 7148 
• Residue Count: 905 
• Unique protein chains: 3

1PBY

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

• DOI: 10.2210/pdb1PBY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Paracoccus denitrificans
• Expression System: Paracoccus denitrificans


• Deposited: 2003-05-15 Released: 2003-09-02 
• Deposition Author(s): Datta, S., Ikeda, T., Kano, K., Mathews, F.S.

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Experimental Data Snapshot

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

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: 12925784 


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
quinohemoprotein amine dehydrogenase 60 kDa subunit	A	489	Paracoccus denitrificans	Mutation(s): 0
Find proteins for Q8VUT0 (Paracoccus denitrificans) Go to UniProtKB:  Q8VUT0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
quinohemoprotein amine dehydrogenase 40 kDa subunit	B	337	Paracoccus denitrificans	Mutation(s): 0
Find proteins for Q8VUS7 (Paracoccus denitrificans) Go to UniProtKB:  Q8VUS7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
quinohemoprotein amine dehydrogenase 9 kDa subunit	C	79	Paracoccus denitrificans	Mutation(s): 0  Gene Names: qhnDH EC: 1.4.99.-
Find proteins for Q8VUS8 (Paracoccus denitrificans) Go to UniProtKB:  Q8VUS8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
TBU	A, B	TERTIARY-BUTYL ALCOHOL 2-METHYL-2-PROPANOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TRW	C	L-PEPTIDE LINKING	C17 H18 N4 O2		TRP

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 = 99.237	α = 90.00
b = 99.237	β = 90.00
c = 213.056	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-15 
• Released Date: 2003-09-02 
• Deposition Author(s): Datta, S., Ikeda, T., Kano, K., Mathews, F.S.

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