1XBN

Crystal structure of a bacterial nitric oxide sensor: an ortholog of mammalian soluble guanylate cyclase heme domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 

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This is version 1.2 of the entry. See complete history. 


Literature

Femtomolar sensitivity of a NO sensor from Clostridium botulinum

Nioche, P., Berka, V., Vipond, J., Minton, N., Tsai, A.-L., Raman, C.S.

(2004) Science 306: 1550-1553

  • DOI: 10.1126/science.1103596
  • Primary Citation of Related Structures:  
    1XBN

  • PubMed Abstract: 

    • Nitric oxide (NO) is extremely toxic to Clostridium botulinum, but its molecular targets are unknown. Here, we identify a heme protein sensor (SONO) that displays femtomolar affinity for NO. The crystal structure of the SONO heme domain reveals a previously undescribed fold and a strategically placed tyrosine residue that modulates heme-nitrosyl coordination ...

    Nitric oxide (NO) is extremely toxic to Clostridium botulinum, but its molecular targets are unknown. Here, we identify a heme protein sensor (SONO) that displays femtomolar affinity for NO. The crystal structure of the SONO heme domain reveals a previously undescribed fold and a strategically placed tyrosine residue that modulates heme-nitrosyl coordination. Furthermore, the domain architecture of a SONO ortholog cloned from Chlamydomonas reinhardtii indicates that NO signaling through cyclic guanosine monophosphate arose before the origin of multicellular eukaryotes. Our findings have broad implications for understanding bacterial responses to NO, as well as for the activation of mammalian NO-sensitive guanylyl cyclase.

    Organizational Affiliation: 

    Structural Biology Research Center and Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis proteinA195Caldanaerobacter subterraneus subsp. tengcongensis MB4Mutation(s): 0 
Gene Names: Tar4, TTE0680
UniProt
Find proteins for Q8RBX6 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Explore Q8RBX6 
Go to UniProtKB:  Q8RBX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RBX6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
OXY
Query on OXY
Download Ideal Coordinates CCD File 
B [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.607α = 90
b = 120.607β = 90
c = 120.607γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
SHELXSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance