1IKE

Crystal Structure of Nitrophorin 4 from Rhodnius Prolixus Complexed with Histamine at 1.5 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Ligand-induced heme ruffling and bent no geometry in ultra-high-resolution structures of nitrophorin 4.

Roberts, S.A.Weichsel, A.Qiu, Y.Shelnutt, J.A.Walker, F.A.Montfort, W.R.

(2001) Biochemistry 40: 11327-11337

  • DOI: 10.1021/bi0109257
  • Primary Citation of Related Structures:  
    1IKJ, 1IKE, 1D2U, 1KOI

  • PubMed Abstract: 
  • The nitrophorins are a family of proteins that use ferric heme to transport nitric oxide (NO) from the salivary glands of blood-sucking insects to their victims, resulting in vasodilation and reduced blood coagulation. We have refined atomic resolution structures of nitrophorin 4 (NP4) from Rhodnius prolixus complexed with NO (1 ...

    The nitrophorins are a family of proteins that use ferric heme to transport nitric oxide (NO) from the salivary glands of blood-sucking insects to their victims, resulting in vasodilation and reduced blood coagulation. We have refined atomic resolution structures of nitrophorin 4 (NP4) from Rhodnius prolixus complexed with NO (1.08 A) and NH(3) (1.15 A), yielding a highly detailed picture of the iron coordination sphere. In NP4-NO, the NO nitrogen is coordinated to iron (Fe-N distance = 1.66 A) and is somewhat bent (Fe-N-O angle = 156 degrees ), with bending occurring in the same plane as the proximal histidine ring. The Fe(NO)(heme)(His) coordination geometry is unusual but consistent with an Fe(III) oxidation state that is stabilized by a highly ruffled heme. Heme ruffling occurs in both structures, apparently due to close contacts between the heme and leucines 123 and 133, but increases on binding NO even though the steric contacts have not changed. We also report the structure of NP4 in complexes with histamine (1.50 A) and imidazole (1.27 A). Unexpectedly, two mobile loops that rearrange to pack against the bound NO in NP4-NO, also rearrange in the NP4-imidazole complex. This conformational change is apparently driven by the nonpolar nature of the NO and imidazole (as bound) ligands. Taken together, the desolvation of the NO binding pocket through a change in protein conformation, and the bending of the NO moiety, possibly through protein-assisted heme ruffling, may lead to a nitrosyl-heme complex that is unusually resistant to autoreduction.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrophorin 4A184Rhodnius prolixusMutation(s): 0 
EC: 1.7.6.1
Find proteins for Q94734 (Rhodnius prolixus)
Explore Q94734 
Go to UniProtKB:  Q94734
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HSM
Query on HSM

Download Ideal Coordinates CCD File 
C [auth A]HISTAMINE
C5 H9 N3
NTYJJOPFIAHURM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.18α = 90
b = 42.52β = 94.35
c = 52.86γ = 90
Software Package:
Software NamePurpose
MADNESSdata collection
SCALAdata scaling
SHELXL-97refinement
MADNESSdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-03-02
    Changes: Other
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2018-04-18
    Changes: Data collection