4HMW

Crystal structure of PhzG from Burkholderia lata 383


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.135 

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This is version 1.2 of the entry. See complete history


Literature

Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis

Xu, N.Ahuja, E.G.Janning, P.Mavrodi, D.V.Thomashow, L.S.Blankenfeldt, W.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1403-1413

  • DOI: https://doi.org/10.1107/S0907444913008354
  • Primary Citation of Related Structures:  
    4HMS, 4HMT, 4HMU, 4HMV, 4HMW, 4HMX

  • PubMed Abstract: 

    Phenazines are redox-active secondary metabolites that many bacteria produce and secrete into the environment. They are broad-specificity antibiotics, but also act as virulence and survival factors in infectious diseases. Phenazines are derived from chorismic acid, but important details of their biosynthesis are still unclear. For example, three two-electron oxidations seem to be necessary in the final steps of the pathway, while only one oxidase, the FMN-dependent PhzG, is conserved in the phenazine-biosynthesis phz operon. Here, crystal structures of PhzG from Pseudomonas fluorescens 2-79 and from Burkholderia lata 383 in complex with excess FMN and with the phenazine-biosynthesis intermediates hexahydrophenazine-1,6-dicarboxylate and tetrahydrophenazine-1-carboxylate generated in situ are reported. Corroborated with biochemical data, these complexes demonstrate that PhzG is the terminal enzyme in phenazine biosynthesis and that its relaxed substrate specificity lets it participate in the generation of both phenazine-1,6-dicarboxylic acid (PDC) and phenazine-1-carboxylic acid (PCA). This suggests that competition between flavin-dependent oxidations through PhzG and spontaneous oxidative decarboxylations determines the ratio of PDC, PCA and unsubstituted phenazine as the products of phenazine biosynthesis. Further, the results indicate that PhzG synthesizes phenazines in their reduced form. These reduced molecules, and not the fully aromatized derivatives, are the likely end products in vivo, explaining why only one oxidase is required in the phenazine-biosynthesis pathway.


  • Organizational Affiliation

    Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxamine 5'-phosphate oxidase
A, B
215Burkholderia lataMutation(s): 0 
Gene Names: Bcep18194_B1572
EC: 1.4.3.5 (PDB Primary Data), 1.10.3.16 (UniProt)
UniProt
Find proteins for Q396C5 (Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383))
Explore Q396C5 
Go to UniProtKB:  Q396C5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ396C5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.135 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.416α = 90
b = 94.416β = 90
c = 51.751γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations