Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39280.29 
• Atom Count: 1918 
• Residue Count: 334 
• Unique protein chains: 1

1V9Z

Crystal Structure of the heme PAS sensor domain of Ec DOS (Ferrous Form)

• DOI: 10.2210/pdb1V9Z/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2004-02-04 Released: 2004-05-25 
• Deposition Author(s): Kurokawa, H., Lee, D.S., Watanabe, M., Sagami, I., Mikami, B., Raman, C.S., Shimizu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.287 
• R-Value Work: 0.244 

Literature

A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor.

Kurokawa, H., Lee, D.S., Watanabe, M., Sagami, I., Mikami, B., Raman, C.S., Shimizu, T.

(2004) J.Biol.Chem. 279: 20186-20193

• PubMed: 14982921 
• DOI: 10.1074/jbc.M314199200
• Primary Citation of Related Structures:  
  1V9Y


• PubMed Abstract: 
  

PAS domains, which have been identified in over 1100 proteins from all three kingdoms of life, convert various input stimuli into signals that propagate to downstream components by modifying protein-protein interactions. One such protein is the Escherichia coli redox sensor, Ec DOS, a phosphodiesterase that degrades cyclic adenosine monophosphate in a redox-dependent manner. Here we report the crystal structures of the heme PAS domain of Ec DOS in both inactive Fe(3+) and active Fe(2+) forms at 1.32 and 1.9 A resolution, respectively. The protein folds into a characteristic PAS domain structure and forms a homodimer. In the Fe(3+) form, the heme iron is ligated to a His-77 side chain and a water molecule. Heme iron reduction is accompanied by heme-ligand switching from the water molecule to a side chain of Met-95 from the FG loop. Concomitantly, the flexible FG loop is significantly rigidified, along with a change in the hydrogen bonding pattern and rotation of subunits relative to each other. The present data led us to propose a novel redox-regulated molecular switch in which local heme-ligand switching may trigger a global "scissor-type" subunit movement that facilitates catalytic control.

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Organizational Affiliation: 

Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Heme pas sensor protein	A, B	167	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: dosP (dos, pdeO, yddU) EC: 3.1.4.52
Find proteins for P76129 (Escherichia coli (strain K12)) Go to UniProtKB:  P76129

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.287 
• R-Value Work: 0.244 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 
  10.15785/SBGRID/133 SBGrid

Unit Cell:

Length (Å)	Angle (°)
a = 46.400	α = 90.00
b = 69.180	β = 90.00
c = 82.450	γ = 90.00

Software Package:

Software Name	Purpose
CNS	phasing
CCP4	data scaling
CNS	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-04 
• Released Date: 2004-05-25 
• Deposition Author(s): Kurokawa, H., Lee, D.S., Watanabe, M., Sagami, I., Mikami, B., Raman, C.S., Shimizu, T.

Revision History 

• Version 1.0: 2004-05-25
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Source and taxonomy, Version format compliance