3B4P

Crystal structure of phenazine biosynthesis protein PhzA/B from Burkholderia cepacia R18194, complex with 2-(cyclohexylamino)benzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis.

Ahuja, E.G.Janning, P.Mentel, M.Graebsch, A.Breinbauer, R.Hiller, W.Costisella, B.Thomashow, L.S.Mavrodi, D.V.Blankenfeldt, W.

(2008) J.Am.Chem.Soc. 130: 17053-17061

  • DOI: 10.1021/ja806325k
  • Primary Citation of Related Structures:  
  • Also Cited By: 3JUQ, 3JUP, 3JUO, 3JUN, 3JUM

  • PubMed Abstract: 
  • Phenazines are redox-active bacterial secondary metabolites that participate in important biological processes such as the generation of toxic reactive oxygen species and the reduction of environmental iron. Their biosynthesis from chorismic acid dep ...

    Phenazines are redox-active bacterial secondary metabolites that participate in important biological processes such as the generation of toxic reactive oxygen species and the reduction of environmental iron. Their biosynthesis from chorismic acid depends on enzymes encoded by the phz operon, but many details of the pathway remain unclear. It previously was shown that phenazine biosynthesis involves the symmetrical head-to-tail double condensation of two identical amino-cyclohexenone molecules to a tricyclic phenazine precursor. While this key step can proceed spontaneously in vitro, we show here that it is catalyzed by PhzA/B, a small dimeric protein of the Delta(5)-3-ketosteroid isomerase/nuclear transport factor 2 family, and we reason that this catalysis is required in vivo. Crystal structures in complex with analogues of the substrate and product suggest that PhzA/B accelerates double imine formation by orienting two substrate molecules and by neutralizing the negative charge of tetrahedral intermediates through protonation. HPLC-coupled NMR reveals that the condensation product rearranges further, which is probably important to prevent back-hydrolysis, and may also be catalyzed within the active site of PhzA/B. The rearranged tricyclic product subsequently undergoes oxidative decarboxylation in a metal-independent reaction involving molecular oxygen. This conversion does not seem to require enzymatic catalysis, explaining why phenazine-1-carboxylic acid is a major product even in strains that use phenazine-1,6-dicarboxylic acid as a precursor of strain-specific phenazine derivatives.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenazine biosynthesis protein A/B
A, B
185Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383)Mutation(s): 0 
Find proteins for Q396C9 (Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383))
Go to UniProtKB:  Q396C9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
3B4
Query on 3B4

Download SDF File 
Download CCD File 
A, B
2-(cyclohexylamino)benzoic acid
C13 H17 N O2
JSXMFCCPQQJLCR-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
A
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3B4Kd: 4000 nM BINDINGMOAD
3B4Kd: 4000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.170 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 64.550α = 90.00
b = 64.550β = 90.00
c = 160.390γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
SHELXDphasing
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance