Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 64.82 kDa 
• Atom Count: 4897 
• Modelled Residue Count: 557 
• Deposited Residue Count: 596 
• Unique protein chains: 1

1XUA

Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens

• PDB DOI: 10.2210/pdb1XUA/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudomonas fluorescens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-26 Released: 2004-11-09 
• Deposition Author(s): Blankenfeldt, W., Kuzin, A.P., Skarina, T., Korniyenko, Y., Tong, L., Bayer, P., Janning, P., Thomashow, L.S., Mavrodi, D.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.187 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 

Literature

Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens

Blankenfeldt, W., Kuzin, A.P., Skarina, T., Korniyenko, Y., Tong, L., Bayer, P., Janning, P., Thomashow, L.S., Mavrodi, D.V.

(2004) Proc Natl Acad Sci U S A 101: 16431-16437

• PubMed: 15545603 
• DOI: 10.1073/pnas.0407371101
• Primary Citation of Related Structures:  
  1SDJ, 1U1V, 1U1W, 1U1X, 1XUA, 1XUB


• PubMed Abstract: 
  

Phenazines produced by Pseudomonas and Streptomyces spp. are heterocyclic nitrogen-containing metabolites with antibiotic, antitumor, and antiparasitic activity. The antibiotic properties of pyocyanin, produced by Pseudomonas aeruginosa, were recognized in the 1890s, although this blue phenazine is now known to be a virulence factor in human disease. Despite their biological significance, the biosynthesis of phenazines is not fully understood. Here we present structural and functional studies of PhzF, an enzyme essential for phenazine synthesis in Pseudomonas spp. PhzF shares topology with diaminopimelate epimerase DapF but lacks the same catalytic residues. The structure of PhzF in complex with its substrate, trans-2,3-dihydro-3-hydroxyanthranilic acid, suggests that it is an isomerase using the conserved glutamate E45 to abstract a proton from C3 of the substrate. The proton is returned to C1 of the substrate after rearrangement of the double-bond system, yielding an enol that converts to the corresponding ketone. PhzF is a dimer that may be bifunctional, providing a shielded cavity for ketone dimerization via double Schiff-base formation to produce the phenazine scaffold. Our proposed mechanism is supported by mass and NMR spectroscopy. The results are discussed in the context of related structures and protein sequences of unknown biochemical function.

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Organizational Affiliation: 

Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenazine biosynthesis protein phzF	A, B	298	Pseudomonas fluorescens	Mutation(s): 0  Gene Names: phzF EC: 5.3.3.17
UniProt
Find proteins for Q51792 (Pseudomonas fluorescens) Explore Q51792  Go to UniProtKB:  Q51792

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HHA	C [auth A], D [auth B]	(2S,3S)-TRANS-2,3-DIHYDRO-3-HYDROXYANTHRANILIC ACID C7 H9 N O3 XBTXTLKLSHACSS-WDSKDSINSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.187 
• R-Value Work: 0.142 
• R-Value Observed: 0.144 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.95	α = 90
b = 100.43	β = 90
c = 57.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-26 
• Released Date: 2004-11-09 
Deposition Author(s): Blankenfeldt, W., Kuzin, A.P., Skarina, T., Korniyenko, Y., Tong, L., Bayer, P., Janning, P., Thomashow, L.S., Mavrodi, D.V.

Revision History  

• Version 1.0: 2004-11-09
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description