5K21

Pyocyanin demethylase

• PDB DOI: https://doi.org/10.2210/pdb5K21/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 = JCM 6387
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-18 Released: 2016-12-07 
• Deposition Author(s): Costa, K.C., Glasser, N.R., Newman, D.K.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.168 

Literature

Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms.

Costa, K.C., Glasser, N.R., Conway, S.J., Newman, D.K.

(2017) Science 355: 170-173

• PubMed: 27940577 
• DOI: https://doi.org/10.1126/science.aag3180
• Primary Citation of Related Structures:  
  5K21


• PubMed Abstract: 
  

  The opportunistic pathogen Pseudomonas aeruginosa produces colorful redox-active metabolites called phenazines, which underpin biofilm development, virulence, and clinical outcomes. Although phenazines exist in many forms, the best studied is pyocyanin. Here, we describe pyocyanin demethylase (PodA), a hitherto uncharacterized protein that oxidizes the pyocyanin methyl group to formaldehyde and reduces the pyrazine ring via an unusual tautomerizing demethylation reaction. Treatment with PodA disrupts P. aeruginosa biofilm formation similarly to DNase, suggesting interference with the pyocyanin-dependent release of extracellular DNA into the matrix. PodA-dependent pyocyanin demethylation also restricts established biofilm aggregate populations experiencing anoxic conditions. Together, these results show that modulating extracellular redox-active metabolites can influence the fitness of a biofilm-forming microorganism.

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Organizational Affiliation: 

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 46.38 kDa 
• Atom Count: 2,905 
• Modelled Residue Count: 366 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyocyanin demethylase	A, B, C	141	Mycolicibacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 = JCM 6387	Mutation(s): 0  Gene Names: MFORT_14352
UniProt
Find proteins for K0V2D8 (Mycolicibacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 = JCM 6387) Explore K0V2D8  Go to UniProtKB:  K0V2D8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6QF	D [auth A], F [auth B], H [auth C]	phenazin-1-ol C12 H8 N2 O SVRNCBGWUMMBQB-UHFFFAOYSA-N
CA	E [auth A], G [auth B], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.33	α = 90
b = 72.98	β = 90
c = 79.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XSCALE	data scaling
PHENIX	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Costa, K.C., Glasser, N.R., Newman, D.K.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	F32AI112248
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	5R01HL117328-03

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-01-11
  Changes: Database references
• Version 1.2: 2017-01-25
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Refinement description
• Version 1.4: 2019-11-20
  Changes: Author supporting evidence