1.0 A Crystal Structure of D129A/L130A Mutant of Nitrophorin 4

Experimental Data Snapshot

  • Resolution: 1.00 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 

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Role of binding site loops in controlling nitric oxide release: structure and kinetics of mutant forms of nitrophorin 4

Maes, E.M.Weichsel, A.Andersen, J.F.Shepley, D.Montfort, W.R.

(2004) Biochemistry 43: 6679-6690

  • DOI: https://doi.org/10.1021/bi049748a
  • Primary Citation of Related Structures:  
    1SXU, 1SXW, 1SXX, 1SXY, 1SY0, 1SY1, 1SY2, 1SY3

  • PubMed Abstract: 

    Nitrophorins are ferric heme proteins that transport nitric oxide (NO) from blood-sucking insects to victims. NO binding is tighter at lower pH values, as found in the insect salivary gland, and weaker at the pH of the victim's tissue, facilitating NO release and subsequent vasodilation. Previous structural analyses of nitrophorin 4 (NP4) from Rhodnius prolixus revealed a substantial NO-induced conformational change involving the A-B and G-H loops, which rearrange to desolvate the distal pocket and pack nonpolar residues against the heme-ligated NO. Previous kinetic analyses revealed a slow, biphasic, and pH-dependent NO release, which was proposed to be associated with loop movements. In this study, we created NP4 mutants D30A and D30N (A-B loop), D129A/L130A (G-H loop), and T121V (distal pocket). Eight crystal structures were determined, including complexes with NO, NH(3), and imidazole, to resolutions as high as 1.0 A. The NO-induced conformational change is largely abolished in the loop mutants, but retained in T121V. Kinetic analyses using stopped-flow spectroscopy revealed the pH dependence for NO release is eliminated for D129A/L130A, considerably reduced for D30A and D30N, but retained for T121V. NO association rates were increased 2-5-fold for T121V, but were unchanged in the loop mutants. Taken together, our findings demonstrate that the pH dependency for NO release is linked to loop dynamics and that solvent reorganization is apparently rate-limiting for formation of the initial iron-nitrosyl bond. Interestingly, the multiphasic kinetic behavior of rNPs was not affected by mutations, and its cause remains unclear.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrophorin 4184Rhodnius prolixusMutation(s): 2 
Find proteins for Q94734 (Rhodnius prolixus)
Explore Q94734 
Go to UniProtKB:  Q94734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94734
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C34 H32 Fe N4 O4
Query on NH4

Download Ideal Coordinates CCD File 
H4 N
Experimental Data & Validation

Experimental Data

  • Resolution: 1.00 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.149α = 90
b = 42.804β = 93.93
c = 52.881γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description