4U9K

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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Literature

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: 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 ...

    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: 

    Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037; marletta@scripps.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NO-binding heme-dependent sensor proteinA, B187Shewanella oneidensis MR-1Mutation(s): 3 
Gene Names: SO_2144
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MNH
Query on MNH
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		MANGANESE PROTOPORPHYRIN IX
C34 H32 Mn N4 O4
UIBYYPDLEONCGQ-RGGAHWMASA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
NO
Query on NO
Download Ideal Coordinates CCD File 
E [auth A]NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYAM		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement

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