4U9B | pdb_00004u9b

Crystal structure of an H-NOX protein from S. oneidensis in the Fe(II)NO ligation state

• PDB DOI: https://doi.org/10.2210/pdb4U9B/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-05 Released: 2014-10-01 
• Deposition Author(s): Herzik Jr., M.A., Jonnalagadda, R., Kuriyan, J., Marletta, M.A.
• Funding Organization(s): American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.203 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

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

• PubMed: 25253889 
• DOI: https://doi.org/10.1073/pnas.1416936111
• Primary Citation 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.

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Organizational Affiliation: 
• Departments of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037;
Departments of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720;
Departments of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; Chemistry, University of California, Berkeley, CA 94720; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720; and Division of Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 22.23 kDa 
• Atom Count: 1,622 
• Modeled Residue Count: 180 
• Deposited Residue Count: 187 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NO-binding heme-dependent sensor protein	A	187	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: SO_2144
UniProt
Find proteins for Q8EF49 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EF49  Go to UniProtKB:  Q8EF49

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NO	C [auth A]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.203 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.636	α = 90
b = 86.716	β = 90
c = 33.822	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Herzik Jr., M.A., Jonnalagadda, R., Kuriyan, J., Marletta, M.A.

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Funding Organization	Location	Grant Number
American Heart Association	United States	11PRE7370086

Revision History  

• 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: 2015-02-04
  Changes: Derived calculations
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary