Crystal structure of an H-NOX protein from S. oneidensis in the Mn(II)NO ligation state, Q154A/Q155A/K156A mutant

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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Structural insights into the role of iron-histidine bond cleavage in nitric oxide-induced activation of H-NOX gas sensor proteins.

Herzik, M.A.Jonnalagadda, R.Kuriyan, J.Marletta, M.A.

(2014) Proc Natl Acad Sci U S A 111: E4156-E4164

  • DOI: https://doi.org/10.1073/pnas.1416936111
  • Primary Citation of Related Structures:  
    4U99, 4U9B, 4U9G, 4U9J, 4U9K

  • PubMed Abstract: 

    Heme-nitric oxide/oxygen (H-NOX) binding domains are a recently discovered family of heme-based gas sensor proteins that are conserved across eukaryotes and bacteria. Nitric oxide (NO) binding to the heme cofactor of H-NOX proteins has been implicated as a regulatory mechanism for processes ranging from vasodilation in mammals to communal behavior in bacteria. A key molecular event during NO-dependent activation of H-NOX proteins is rupture of the heme-histidine bond and formation of a five-coordinate nitrosyl complex. Although extensive biochemical studies have provided insight into the NO activation mechanism, precise molecular-level details have remained elusive. In the present study, high-resolution crystal structures of the H-NOX protein from Shewanella oneidensis in the unligated, intermediate six-coordinate and activated five-coordinate, NO-bound states are reported. From these structures, it is evident that several structural features in the heme pocket of the unligated protein function to maintain the heme distorted from planarity. NO-induced scission of the iron-histidine bond triggers structural rearrangements in the heme pocket that permit the heme to relax toward planarity, yielding the signaling-competent NO-bound conformation. Here, we also provide characterization of a nonheme metal coordination site occupied by zinc in an H-NOX protein.

  • Organizational Affiliation

    Departments of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720;

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NO-binding heme-dependent sensor protein
A, B
187Shewanella oneidensis MR-1Mutation(s): 3 
Gene Names: SO_2144
Find proteins for Q8EF49 (Shewanella oneidensis (strain MR-1))
Explore Q8EF49 
Go to UniProtKB:  Q8EF49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EF49
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.303α = 90
b = 164.303β = 90
c = 101.679γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
American Heart AssociationUnited States11PRE7370086

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2014-10-15
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy