1OR4

Crystal Structure of HemAT sensor domain from B.subtilis in the cyano-liganded form

• PDB DOI: https://doi.org/10.2210/pdb1OR4/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-03-11 Released: 2003-09-23 
• Deposition Author(s): Zhang, W., Phillips Jr., G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.258 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry.

Zhang, W., Phillips, G.N.

(2003) Structure 11: 1097-1110

• PubMed: 12962628 
• DOI: https://doi.org/10.1016/s0969-2126(03)00169-2
• Primary Citation of Related Structures:  
  1OR4, 1OR6


• PubMed Abstract: 
  

  Much is now known about chemotaxis signaling transduction for Escherichia coli and Salmonella typhimurium. The mechanism of chemotaxis of Bacillus subtilis is, in a sense, reversed. Attractant binding strengthens the activity of histidine kinase in B. subtilis, instead of an inhibition reaction. The HemAT from B. subtilis can detect oxygen and transmit the signal to regulatory proteins that control the direction of flagella rotation. We have determined the crystal structures of the HemAT sensor domain in liganded and unliganded forms at 2.15 A and 2.7 A resolution, respectively. The liganded structure reveals a highly symmetrical organization. Tyrosine70 shows distinct conformational changes on one subunit when ligands are removed. Our study suggests that disruption of the symmetry of HemAT plays an important role in initiating the chemotaxis signaling transduction cascade.

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Organizational Affiliation: 

Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 42.97 kDa 
• Atom Count: 2,960 
• Modelled Residue Count: 327 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme-based aerotactic transducer hemAT	A, B	178	Bacillus subtilis	Mutation(s): 0  Gene Names: yhfV
UniProt
Find proteins for O07621 (Bacillus subtilis (strain 168)) Explore O07621  Go to UniProtKB:  O07621

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CYN	C [auth A], E [auth B]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.258 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.994	α = 90
b = 80.117	β = 90
c = 85.944	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-23 
Deposition Author(s): Zhang, W., Phillips Jr., G.N.

Revision History  

• Version 1.0: 2003-09-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations